Debugging simulation failures
Objective: Demonstrate common simulation failures and give some hints for interpreting, debugging, and fixing them.
[1]:
%matplotlib inline
import os
from contextlib import suppress
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
from amici import (
SbmlImporter,
import_model_module,
)
from amici.importers.petab.v1 import (
import_petab_problem,
)
from amici.sim.sundials import (
AMICI_SUCCESS,
ExpData,
SensitivityMethod,
SensitivityOrder,
SteadyStateSensitivityMode,
run_simulation,
simulation_status_to_str,
unscale_parameter,
)
from amici.sim.sundials.petab.v1 import (
EDATAS,
RDATAS,
simulate_petab,
)
from amici.sim.sundials.plotting import plot_jacobian, plot_state_trajectories
from petab.v1.sbml import get_sbml_model
try:
import benchmark_models_petab
except ModuleNotFoundError:
# install `benchmark_models_petab` if necessary
%pip install -q -e "git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python&egg=benchmark_models_petab"
try:
import benchmark_models_petab
except ModuleNotFoundError:
print("** Please restart the kernel. **")
Overview
In the following, we will simulate models contained in the PEtab Benchmark Collection and the SBML test suite to demonstrate a number of simulation failures to analyze and fix them. We use the PEtab format, as it makes model import and simulation much easier, but everything illustrated here, also applies to plain SBML or PySB import.
Note that, due to numerical issues, the examples below may not be fully reproducible on every system.
If any simulation failures occur, they will be printed via Python logging. Additionally, they will be stored in ReturnData.messages.
Programmatically, simulation success can be checked via ReturnDataView.status. In case of a successful simulation, and only then, this value corresponds to amici.AMICI_SUCCESS. In case of a simulation error, all quantities in ReturnData/ReturnDataView will be reported up to the time of failure, the rest will be NaN. The likelihood and it’s gradient will always be NaN in case of failure.
AMICI_TOO_MUCH_WORK - mxstep steps taken before reaching tout
Let’s run a simulation:
[2]:
petab_problem = benchmark_models_petab.get_problem("Fujita_SciSignal2010")
amici_model = import_petab_problem(petab_problem, verbose=False, compile_=None)
np.random.seed(2991)
problem_parameters = dict(
zip(
petab_problem.x_free_ids,
petab_problem.sample_parameter_startpoints(n_starts=1)[0],
)
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert [simulation_status_to_str(rdata.status) for rdata in res[RDATAS]] == [
"AMICI_SUCCESS",
"AMICI_SUCCESS",
"AMICI_SUCCESS",
"AMICI_TOO_MUCH_WORK",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
]
2026-09-03 09:11:24.167 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.168 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.169 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.172 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.172 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:24.173 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:24.174 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.174 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.175 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.175 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.176 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:24.176 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:24.177 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.178 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.179 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.179 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.180 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:24.180 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:24.181 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.181 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.182 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.182 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.183 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.183 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.184 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.184 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.185 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.185 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.186 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.186 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.187 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.188 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.188 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.189 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.189 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
2026-09-03 09:11:24.190 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
2026-09-03 09:11:24.352 - amici.sim.sundials._swig_wrappers - DEBUG - [condition_step_03_0][cvodes:CVode:TOO_MUCH_WORK] At t = 3031.8, mxstep steps taken before reaching tout.
2026-09-03 09:11:24.353 - amici.sim.sundials._swig_wrappers - ERROR - [condition_step_03_0][FORWARD_FAILURE] AMICI forward simulation failed at t = 3031.8: AMICI failed to integrate the forward problem
Status: ['AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_TOO_MUCH_WORK', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN']
What happened?
AMICI failed to integrate the forward problem. The problem occurred for only one simulation condition, condition_step_03_0. The issue occurred at \(t = 3031.8\), where the CVODES reached the maximum number of steps.
How to address?
The number of steps the solver has to take is closely related to the chosen error tolerance. More accurate results, more steps. Therefore, this problem can be solved in two ways:
Increasing the maximum number of steps via Solver.set_max_steps. Note that this will increase the time required for simulation, and that simulation may still fail eventually. Sometimes it may be preferable to not increase this limit but rather fail fast. Also note that increasing the number of allowed steps increase RAM requirements (even if fewer steps are actually taken), so don’t set this to ridiculously large values in order to avoid this error.
Reducing the number of steps CVODES has to take. This is determined by the required error tolerance. There are various solver error tolerances than can be adjusted. The most relevant ones are those controlled via Solver.set_relative_tolerance() and Solver.set_absolute_tolerance().
So, let’s fix that:
[3]:
# let's increase the allowed number of steps by 10x:
print("Increasing allowed number of steps ...")
amici_solver = amici_model.create_solver()
amici_solver.set_max_steps(10 * amici_solver.get_max_steps())
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert all(rdata.status == AMICI_SUCCESS for rdata in res[RDATAS])
print("Simulations finished successfully.")
print()
# let's relax the relative error tolerance by a factor of 50
print("Relaxing relative error tolerance ...")
amici_solver = amici_model.create_solver()
amici_solver.set_relative_tolerance(50 * amici_solver.get_relative_tolerance())
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert all(rdata.status == AMICI_SUCCESS for rdata in res[RDATAS])
print("Simulations finished successfully.")
2026-09-03 09:11:24.429 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.430 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.431 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.432 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.433 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:24.434 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:24.435 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.436 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.437 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.438 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.439 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:24.439 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:24.441 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.441 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.442 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.442 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.443 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:24.443 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:24.444 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.445 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.445 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.446 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.446 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.446 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.447 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.448 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.448 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.449 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.449 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.450 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.450 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.451 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.451 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.452 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.452 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
2026-09-03 09:11:24.453 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
Increasing allowed number of steps ...
Status: ['AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS']
Simulations finished successfully.
Relaxing relative error tolerance ...
2026-09-03 09:11:24.661 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.662 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.663 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.664 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.665 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:24.666 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:24.667 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.667 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.668 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.668 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.669 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:24.669 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:24.670 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.670 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.671 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.671 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.672 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:24.672 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:24.673 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.674 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.675 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.675 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.676 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.676 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.677 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.677 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.678 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.678 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.679 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.679 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:24.680 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:24.680 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:24.681 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:24.681 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:24.682 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
2026-09-03 09:11:24.682 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
Status: ['AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS']
Simulations finished successfully.
Internal t = [...] and h = [...] are such that t + h = t on the next step
Let’s run a simulation:
[4]:
petab_problem = benchmark_models_petab.get_problem("Crauste_CellSystems2017")
amici_model = import_petab_problem(petab_problem, verbose=False)
np.random.seed(1)
problem_parameters = dict(
zip(
petab_problem.x_free_ids,
petab_problem.sample_parameter_startpoints(n_starts=1)[0],
)
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert [simulation_status_to_str(rdata.status) for rdata in res[RDATAS]] == [
"AMICI_TOO_MUCH_WORK"
]
2026-09-03 09:11:40.088 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'delta_EL': 'delta_EL', 'delta_LM': 'delta_LM', 'delta_NE': 'delta_NE', 'mu_EE': 'mu_EE', 'mu_LE': 'mu_LE', 'mu_LL': 'mu_LL', 'mu_N': 'mu_N', 'mu_P': 'mu_P', 'mu_PE': 'mu_PE', 'mu_PL': 'mu_PL', 'rho_E': 'rho_E', 'rho_P': 'rho_P', 'noiseParameter1_observable_EarlyEffector': 1540, 'noiseParameter1_observable_LateEffector': 2705, 'noiseParameter1_observable_Memory': 7909, 'noiseParameter1_observable_Naive': 64}, {}, {'delta_EL': 'log10', 'delta_LM': 'log10', 'delta_NE': 'log10', 'mu_EE': 'log10', 'mu_LE': 'log10', 'mu_LL': 'log10', 'mu_N': 'log10', 'mu_P': 'log10', 'mu_PE': 'log10', 'mu_PL': 'log10', 'rho_E': 'log10', 'rho_P': 'log10', 'noiseParameter1_observable_EarlyEffector': 'lin', 'noiseParameter1_observable_LateEffector': 'lin', 'noiseParameter1_observable_Memory': 'lin', 'noiseParameter1_observable_Naive': 'lin'})
2026-09-03 09:11:40.089 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:40.089 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {}
2026-09-03 09:11:40.090 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:40.090 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'delta_EL': 'delta_EL', 'delta_LM': 'delta_LM', 'delta_NE': 'delta_NE', 'mu_EE': 'mu_EE', 'mu_LE': 'mu_LE', 'mu_LL': 'mu_LL', 'mu_N': 'mu_N', 'mu_P': 'mu_P', 'mu_PE': 'mu_PE', 'mu_PL': 'mu_PL', 'rho_E': 'rho_E', 'rho_P': 'rho_P', 'noiseParameter1_observable_EarlyEffector': 1540, 'noiseParameter1_observable_LateEffector': 2705, 'noiseParameter1_observable_Memory': 7909, 'noiseParameter1_observable_Naive': 64}
2026-09-03 09:11:40.091 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'delta_EL': 'delta_EL', 'delta_LM': 'delta_LM', 'delta_NE': 'delta_NE', 'mu_EE': 'mu_EE', 'mu_LE': 'mu_LE', 'mu_LL': 'mu_LL', 'mu_N': 'mu_N', 'mu_P': 'mu_P', 'mu_PE': 'mu_PE', 'mu_PL': 'mu_PL', 'rho_E': 'rho_E', 'rho_P': 'rho_P', 'noiseParameter1_observable_EarlyEffector': 1540, 'noiseParameter1_observable_LateEffector': 2705, 'noiseParameter1_observable_Memory': 7909, 'noiseParameter1_observable_Naive': 64}
2026-09-03 09:11:40.121 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.121 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.123 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.123 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.124 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.124 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.125 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.125 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.126 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.126 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] Internal t = 0.330112 and h = 2.06577e-17 are such that t + h = t on the next step. The solver will continue anyway.
2026-09-03 09:11:40.127 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:WARNING] The above warning has been issued mxhnil times and will not be issued again for this problem.
2026-09-03 09:11:40.127 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:TOO_MUCH_WORK] At t = 0.330112, mxstep steps taken before reaching tout.
2026-09-03 09:11:40.128 - amici.sim.sundials._swig_wrappers - ERROR - [model1_data1][FORWARD_FAILURE] AMICI forward simulation failed at t = 0.330112: AMICI failed to integrate the forward problem
Status: ['AMICI_TOO_MUCH_WORK']
What happened?
The forward simulation failed because the AMICI solver exceeded the maximum number of steps. Unlike in the previous case of mxstep steps taken before reaching tout (see above), here we got several additional warnings that the current step size \(h\) is numerically zero.
How to address?
The warning Internal t = [...] and h = [...] are such that t + h = t on the next step tells us that the solver is not able to move forward. The solver may be able to recover from that, but not always.
Let’s look at the state trajectories to see what’s going on. Such a tiny step size is usually related to very fast dynamics. We repeat the simulation with additional timepoints before the point of failure:
[5]:
# Create a copy of this simulation condition
edata = ExpData(res[EDATAS][0])
edata.set_timepoints(np.linspace(0, 0.33011, 5000))
amici_solver = amici_model.create_solver()
rdata = run_simulation(amici_model, amici_solver, edata)
# Visualize state trajectories
plot_state_trajectories(rdata)
plt.yscale("log")
We can see a steep increase for Pathogen just before the error occurs. Let’s zoom in:
[6]:
plt.plot(rdata.t, rdata.by_id("Pathogen"))
plt.xlabel("time")
plt.ylabel("Pathogen");
The solver is unable to handle such a steep increase. There is not much we can do. Increasing the tolerances will let the solver proceed a bit further, but this is usually not enough. Most likely there is a problem in the model or in the choice of parameter values.
the error test failed repeatedly or with |h| = hmin
Let’s run a simulation:
[7]:
petab_problem = benchmark_models_petab.get_problem("Fujita_SciSignal2010")
amici_model = import_petab_problem(petab_problem, verbose=False)
np.random.seed(4920)
problem_parameters = dict(
zip(
petab_problem.x_free_ids,
petab_problem.sample_parameter_startpoints(n_starts=1)[0],
)
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert [simulation_status_to_str(rdata.status) for rdata in res[RDATAS]] == [
"AMICI_SUCCESS",
"AMICI_ERR_FAILURE",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
]
2026-09-03 09:11:41.496 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:41.497 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:41.498 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:41.499 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:41.500 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:41.501 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:41.502 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:41.503 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:41.504 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:41.504 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:41.506 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:41.506 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:41.508 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:41.509 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:41.510 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:41.510 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:41.511 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:41.513 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:41.514 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:41.515 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:41.515 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:41.516 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:41.516 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:41.517 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:41.518 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:41.519 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:41.519 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:41.521 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:41.522 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:41.523 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:41.524 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:41.524 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:41.525 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:41.525 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:41.526 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
2026-09-03 09:11:41.526 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
2026-09-03 09:11:41.630 - amici.sim.sundials._swig_wrappers - DEBUG - [condition_step_00_3][cvodes:cvHandleFailure:ERR_FAILURE] At t = 429.232 and h = 7.75194e-05, the error test failed repeatedly or with |h| = hmin.
2026-09-03 09:11:41.631 - amici.sim.sundials._swig_wrappers - ERROR - [condition_step_00_3][FORWARD_FAILURE] AMICI forward simulation failed at t = 429.232: AMICI failed to integrate the forward problem
Status: ['AMICI_SUCCESS', 'AMICI_ERR_FAILURE', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN']
What happened?
AMICI failed to integrate the forward problem. The problem occurred for only one simulation condition, condition_step_00_3. The issue occurred at \(t = 429.232\), where the error test failed. This means, the solver is unable to take a step of non-zero size without violating the chosen error tolerances.
How to address?
The step size is computed based on the Jacobian. Inspecting ReturnData.J shows us that we have rather large values in the Jacobian:
[8]:
rdata = res[RDATAS][1]
# Show Jacobian as heatmap
plot_jacobian(rdata)
print(f"largest absolute Jacobian value: {np.max(np.abs(rdata.J)):.3g}")
largest absolute Jacobian value: 4.09e+05
In this case, the default relative error tolerance may be too high and lead too large absolute errors.
Let’s retry simulation using stricter tolerances:
[9]:
# set stricter relative error tolerance
amici_solver = amici_model.create_solver()
amici_solver.set_relative_tolerance(amici_solver.get_relative_tolerance() / 10)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert all(rdata.status == AMICI_SUCCESS for rdata in res[RDATAS])
print("Simulations finished successfully.")
2026-09-03 09:11:42.109 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:42.111 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:42.112 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.1, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:42.113 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:42.114 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:42.114 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.035}
2026-09-03 09:11:42.115 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:42.116 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:42.117 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 0.3, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:42.118 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:42.118 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:42.119 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.025}
2026-09-03 09:11:42.119 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:42.120 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:42.120 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 1.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:42.121 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:42.121 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:42.122 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.075}
2026-09-03 09:11:42.122 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:42.123 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:42.125 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 3.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:42.126 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:42.126 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:42.127 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.02, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:42.128 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:42.128 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:42.129 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 10.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:42.129 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:42.130 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:42.130 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.08}
2026-09-03 09:11:42.131 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0, 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}, {}, {'EGFR_turnover': 'log10', 'init_AKT': 'log10', 'init_EGFR': 'log10', 'init_S6': 'log10', 'reaction_1_k1': 'log10', 'reaction_1_k2': 'log10', 'reaction_2_k1': 'log10', 'reaction_2_k2': 'log10', 'reaction_3_k1': 'log10', 'reaction_4_k1': 'log10', 'reaction_5_k1': 'log10', 'reaction_5_k2': 'log10', 'reaction_6_k1': 'log10', 'reaction_7_k1': 'log10', 'reaction_8_k1': 'log10', 'reaction_9_k1': 'log10', 'EGF_0': 'lin', 'EGF_rate': 'lin', 'EGF_end': 'lin', 'observableParameter1_pAkt_tot': 'log10', 'observableParameter1_pEGFR_tot': 'log10', 'observableParameter1_pS6_tot': 'log10', 'noiseParameter1_pAkt_tot': 'lin', 'noiseParameter1_pEGFR_tot': 'lin', 'noiseParameter1_pS6_tot': 'lin'})
2026-09-03 09:11:42.131 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:11:42.132 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'EGF_0': 30.0, 'EGF_rate': 0.0, 'EGF_end': 3600.0}
2026-09-03 09:11:42.132 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:11:42.133 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
2026-09-03 09:11:42.133 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'EGFR_turnover': 'EGFR_turnover', 'init_AKT': 'init_AKT', 'init_EGFR': 'init_EGFR', 'init_S6': 'init_S6', 'reaction_1_k1': 'reaction_1_k1', 'reaction_1_k2': 'reaction_1_k2', 'reaction_2_k1': 'reaction_2_k1', 'reaction_2_k2': 'reaction_2_k2', 'reaction_3_k1': 'reaction_3_k1', 'reaction_4_k1': 'reaction_4_k1', 'reaction_5_k1': 'reaction_5_k1', 'reaction_5_k2': 'reaction_5_k2', 'reaction_6_k1': 'reaction_6_k1', 'reaction_7_k1': 'reaction_7_k1', 'reaction_8_k1': 'reaction_8_k1', 'reaction_9_k1': 'reaction_9_k1', 'observableParameter1_pAkt_tot': 'scaling_pAkt_tot', 'observableParameter1_pEGFR_tot': 'scaling_pEGFR_tot', 'observableParameter1_pS6_tot': 'scaling_pS6_tot', 'noiseParameter1_pAkt_tot': 0.01, 'noiseParameter1_pEGFR_tot': 0.01, 'noiseParameter1_pS6_tot': 0.07}
Status: ['AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS']
Simulations finished successfully.
Cvode routine CVode returned a root after reinitialization
Let’s run a simulation:
[ ]:
[10]:
# retrieve and import the SBML model
if "imported_00885" not in globals():
sbml_reader, sbml_document, sbml_model = get_sbml_model(
"https://raw.githubusercontent.com/sbmlteam/sbml-test-suite/7ab011efe471877987b5d6dcba8cc19a6ff71254/cases/semantic/00885/00885-sbml-l3v2.xml"
)
SbmlImporter(sbml_model).sbml2amici(
model_name="sbml_00885", output_dir="amici_models/sbml_00885"
)
imported_00885 = True
amici_model = import_model_module(
"sbml_00885", "amici_models/sbml_00885"
).get_model()
# run the simulation
amici_solver = amici_model.create_solver()
amici_solver.set_sensitivity_method(SensitivityMethod.forward)
amici_solver.set_sensitivity_order(SensitivityOrder.first)
amici_model.set_timepoints(np.linspace(0, 6, 51))
rdata = run_simulation(amici_model, amici_solver)
print("Status:", simulation_status_to_str(rdata.status))
assert simulation_status_to_str(rdata.status) == "AMICI_ERROR"
2026-09-03 09:11:59.055 - amici.sim.sundials._swig_wrappers - ERROR - [OTHER] AMICI simulation failed: CVODE routine CVode returned a root after reinitialization at t=2.107007. The initial step-size after the event or Heaviside function is too small. To fix this, adjust absolute or relative tolerances! failed with error code 2.
Status: AMICI_ERROR
What happened?
The simulation failed because the initial step-size after an event or Heaviside function was too small. The error occurred around t=2.1.
How to address?
The error message already suggests a fix for this situation, so let’s try decreasing the relative tolerance:
[11]:
amici_solver = amici_model.create_solver()
amici_solver.set_sensitivity_method(SensitivityMethod.forward)
amici_solver.set_sensitivity_order(SensitivityOrder.first)
amici_solver.set_relative_tolerance(1e-15)
amici_model.set_timepoints(np.linspace(0, 6, 51))
rdata = run_simulation(amici_model, amici_solver)
print("Status:", simulation_status_to_str(rdata.status))
assert simulation_status_to_str(rdata.status) == "AMICI_SUCCESS"
Status: AMICI_SUCCESS
Sometimes this problem can also be solved be increasing tolerances or by slightly changing the output timepoints.
AMICI encountered a NaN / Inf value for [...]
Let’s run a simulation:
[12]:
petab_problem = benchmark_models_petab.get_problem("Borghans_BiophysChem1997")
amici_model = import_petab_problem(petab_problem, verbose=False)
np.random.seed(18)
problem_parameters = dict(
zip(
petab_problem.x_free_ids,
petab_problem.sample_parameter_startpoints(n_starts=1)[0],
)
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert [simulation_status_to_str(rdata.status) for rdata in res[RDATAS]] == [
"AMICI_FIRST_RHSFUNC_ERR"
]
2026-09-03 09:12:14.985 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'K2': 'K2', 'K_par': 'K_par', 'Ka': 'Ka', 'Kd': 'Kd', 'Kf': 'Kf', 'Kp': 'Kp', 'Ky': 'Ky', 'Kz': 'Kz', 'Vd': 'Vd', 'Vm2': 'Vm2', 'Vm3': 'Vm3', 'Vp': 'Vp', 'beta_par': 'beta_par', 'epsilon_par': 'epsilon_par', 'init_A_state': 'init_A_state', 'init_Y_state': 'init_Y_state', 'init_Z_state': 'init_Z_state', 'n_par': 'n_par', 'v0': 'v0', 'v1': 'v1', 'observableParameter1_Ca': 'offset', 'observableParameter2_Ca': 'scale', 'noiseParameter1_Ca': 'sigma'}, {}, {'K2': 'log10', 'K_par': 'log10', 'Ka': 'log10', 'Kd': 'log10', 'Kf': 'log10', 'Kp': 'log10', 'Ky': 'log10', 'Kz': 'log10', 'Vd': 'log10', 'Vm2': 'log10', 'Vm3': 'log10', 'Vp': 'log10', 'beta_par': 'log10', 'epsilon_par': 'log10', 'init_A_state': 'lin', 'init_Y_state': 'lin', 'init_Z_state': 'lin', 'n_par': 'log10', 'v0': 'log10', 'v1': 'log10', 'observableParameter1_Ca': 'log10', 'observableParameter2_Ca': 'log10', 'noiseParameter1_Ca': 'log10'})
2026-09-03 09:12:14.985 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:12:14.986 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {}
2026-09-03 09:12:14.986 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:12:14.987 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'K2': 'K2', 'K_par': 'K_par', 'Ka': 'Ka', 'Kd': 'Kd', 'Kf': 'Kf', 'Kp': 'Kp', 'Ky': 'Ky', 'Kz': 'Kz', 'Vd': 'Vd', 'Vm2': 'Vm2', 'Vm3': 'Vm3', 'Vp': 'Vp', 'beta_par': 'beta_par', 'epsilon_par': 'epsilon_par', 'init_A_state': 'init_A_state', 'init_Y_state': 'init_Y_state', 'init_Z_state': 'init_Z_state', 'n_par': 'n_par', 'v0': 'v0', 'v1': 'v1', 'observableParameter1_Ca': 'offset', 'observableParameter2_Ca': 'scale', 'noiseParameter1_Ca': 'sigma'}
2026-09-03 09:12:14.987 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'K2': 'K2', 'K_par': 'K_par', 'Ka': 'Ka', 'Kd': 'Kd', 'Kf': 'Kf', 'Kp': 'Kp', 'Ky': 'Ky', 'Kz': 'Kz', 'Vd': 'Vd', 'Vm2': 'Vm2', 'Vm3': 'Vm3', 'Vp': 'Vp', 'beta_par': 'beta_par', 'epsilon_par': 'epsilon_par', 'init_A_state': 'init_A_state', 'init_Y_state': 'init_Y_state', 'init_Z_state': 'init_Z_state', 'n_par': 'n_par', 'v0': 'v0', 'v1': 'v1', 'observableParameter1_Ca': 'offset', 'observableParameter2_Ca': 'scale', 'noiseParameter1_Ca': 'sigma'}
2026-09-03 09:12:15.166 - amici.sim.sundials._swig_wrappers - WARNING - [model1_data1][AMICI:NaN] AMICI encountered a NaN value for xdot[2] (A_state) at t=0.000000
2026-09-03 09:12:15.166 - amici.sim.sundials._swig_wrappers - WARNING - [model1_data1][AMICI:NaN] AMICI encountered a NaN value for w[6] (flux_v7_v_6) at t=0.000000
2026-09-03 09:12:15.168 - amici.sim.sundials._swig_wrappers - DEBUG - [model1_data1][cvodes:CVode:FIRST_RHSFUNC_ERR] The right-hand side routine failed at the first call.
2026-09-03 09:12:15.169 - amici.sim.sundials._swig_wrappers - ERROR - [model1_data1][FORWARD_FAILURE] AMICI forward simulation failed at t = 0: AMICI failed to integrate the forward problem
Status: ['AMICI_FIRST_RHSFUNC_ERR']
What happened?
The forward simulation failed because AMICI encountered a NaN value when simulating condition model1_data1. Then NaNs occurred in \(\dot x\) and \(w\) (model expressions, such as reaction fluxes or assignment rules). Furthermore, the failure occurred at the first call, so at \(t = t_0\) (here: \(t = 0\)).
How to address?
The NaN in \(\dot x\) is most likely a consequence of the one in \(w\). (A subset of) the dependency tree looks something like:
Always look for the most basic (furthest up) model quantities. In cases where non-finite values occur in expressions further down, rerunning the simulation after calling Model.setAlwaysCheckFinite(True) may give some further hints on where the issue originates.
The NaN in \(w\) occurred for flux_v7_v_6 (see error log), i.e., when computing the reaction flux for reaction v7_v_6. As \(w\) only depends on \((t, p, k, x)\) and no non-finite values have been reported for those, the issue has to be in the respective flux equation.
Let’s look at that expression. This can either be done by inspecting the underlying SBML model (e.g., using COPASI), or by checking the generated model code:
[13]:
# model source code location
model_src_dir = Path(amici_model.module.__file__).parents[1]
# find the problematic expression in the model source code
!grep flux_v7_v_6 {model_src_dir}/w.cpp
flux_v7_v_6 = std::pow(A_state, 2)*Vd*std::pow(Z_state, n_par)/((std::pow(A_state, 2) + std::pow(Kp, 2))*(std::pow(Kd, n_par) + std::pow(Z_state, n_par))); // w[6]
What could go wrong? We can obtain NaN from any of these symbols being NaN, or through division by zero.
Let’s let’s check the denominator first:
\[(A\_state^2 + Kp^2)*(Kd^{n\_par} + Z\_state^{n\_par})\]
A_state and Z_state are state variables, Kd, K_p, and n_par are parameters.
As the error occurred at \(t = t_0\), let’s ensure the initial state is non-zero and finite:
[14]:
rdata = res[RDATAS][0]
edata = res[EDATAS][0]
# check initial states
x0 = dict(zip(amici_model.get_state_ids(), rdata.x0))
print(f"{x0=}")
x0={'Z_state': np.float64(0.6869701913398437), 'Y_state': np.float64(0.2977237418558598), 'A_state': np.float64(0.1116031306650328)}
The initial states are fine - the first multiplicand is non-zero, as \(x_0\) was non-zero.
So let’s check the parameter values occurring in the second multiplicand:
[15]:
# we have to account for the chosen parameter scale
from itertools import starmap
unscaled_parameter = dict(
zip(
amici_model.get_free_parameter_ids(),
starmap(unscale_parameter, zip(edata.free_parameters, edata.pscale)),
)
)
print(dict((p, unscaled_parameter[p]) for p in ("Kd", "Kp", "n_par")))
{'Kd': 0.028491925689008366, 'Kp': 1002.513636749445, 'n_par': 7816.430091706722}
Considering that n_par occurs as exponent, it’s magnitude looks pretty high. This term is very likely causing the problem - let’s check:
[16]:
print(
f"{x0['Z_state']**unscaled_parameter['n_par'] + unscaled_parameter['Kd']**unscaled_parameter['n_par']=}"
)
x0['Z_state']**unscaled_parameter['n_par'] + unscaled_parameter['Kd']**unscaled_parameter['n_par']=np.float64(0.0)
Indeed, no way we can fix this for the given model. This was most likely an unrealistic parameter value, originating from a too high upper parameter bound for n_par. Therefore, if this error occurs during optimization, a first step could be adapting the respective parameter bounds. In other cases, this may be a result of unfortunate arrangement of model expressions, which can sometimes be solved by passing a suitable simplification function to the model import.
Steady state sensitivity computation failed due to unsuccessful factorization of RHS Jacobian
Let’s run a simulation:
[17]:
petab_problem = benchmark_models_petab.get_problem("Blasi_CellSystems2016")
with suppress(KeyError):
del os.environ["AMICI_EXPERIMENTAL_SBML_NONCONST_CLS"]
amici_model = import_petab_problem(
petab_problem,
verbose=False,
compile_=True,
model_name="Blasi_CellSystems2016_1",
)
amici_solver = amici_model.create_solver()
amici_solver.set_sensitivity_method(SensitivityMethod.forward)
amici_solver.set_sensitivity_order(SensitivityOrder.first)
amici_model.set_steady_state_sensitivity_mode(
SteadyStateSensitivityMode.newtonOnly
)
np.random.seed(2020)
problem_parameters = dict(
zip(
petab_problem.x_free_ids,
petab_problem.sample_parameter_startpoints(n_starts=1)[0],
)
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
# hard to reproduce on GHA
if os.getenv("GITHUB_ACTIONS") is None:
assert [
simulation_status_to_str(rdata.status) for rdata in res[RDATAS]
] == ["AMICI_ERROR"]
2026-09-03 09:12:32.069 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'d': np.float64(0.0), 'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}, {}, {'d': 'log10', 'a_k8': 'log10', 'a_k5_k5k12': 'log10', 'a_k12_k5k12': 'log10', 'a_k16_k12k16': 'log10', 'a_k5k12_k5k8k12': 'log10', 'a_k12k16_k8k12k16': 'log10', 'a_k8k12k16_4ac': 'log10', 'a_basal': 'log10', 'noiseParameter1_observable_0ac': 'log10', 'noiseParameter1_observable_4ac': 'log10', 'noiseParameter1_observable_k12': 'log10', 'noiseParameter1_observable_k12k16': 'log10', 'noiseParameter1_observable_k16': 'log10', 'noiseParameter1_observable_k5': 'log10', 'noiseParameter1_observable_k5k12': 'log10', 'noiseParameter1_observable_k5k12k16': 'log10', 'noiseParameter1_observable_k5k16': 'lin', 'noiseParameter1_observable_k5k8': 'log10', 'noiseParameter1_observable_k5k8k12': 'log10', 'noiseParameter1_observable_k5k8k16': 'log10', 'noiseParameter1_observable_k8': 'log10', 'noiseParameter1_observable_k8k12': 'log10', 'noiseParameter1_observable_k8k12k16': 'log10', 'noiseParameter1_observable_k8k16': 'log10'})
2026-09-03 09:12:32.070 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:12:32.071 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'d': np.float64(0.0)}
2026-09-03 09:12:32.072 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:12:32.073 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}
2026-09-03 09:12:32.074 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}
2026-09-03 09:12:32.099 - amici.sim.sundials._swig_wrappers - ERROR - [control][OTHER] AMICI simulation failed: Steady state sensitivity computation failed due to unsuccessful factorization of RHS Jacobian
Status: ['AMICI_ERROR']
What happened?
AMICI failed to compute steady-state sensitivities, because it was not able to factorize the Jacobian.
How to address?
This is most likely a result of a singular Jacobian. Let’s check the condition number:
[18]:
rdata = res[RDATAS][0]
np.linalg.cond(rdata.J)
[18]:
np.float64(1.7144291755459935e+18)
Indeed, the condition number shows that the Jacobian is numerically singular. If this happens consistently, it is usually due to conserved quantities in the model.
There are two ways we can address that:
Use numerical integration to compute sensitivities, for which a singular Jacobian is not an issue. This is, usually, slower, though.
Remove any conserved quantities.
Let’s try both approaches:
[19]:
# use numerical integration
amici_model.set_steady_state_sensitivity_mode(
SteadyStateSensitivityMode.integrationOnly
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert all(rdata.status == AMICI_SUCCESS for rdata in res[RDATAS])
2026-09-03 09:12:32.168 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'d': np.float64(0.0), 'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}, {}, {'d': 'log10', 'a_k8': 'log10', 'a_k5_k5k12': 'log10', 'a_k12_k5k12': 'log10', 'a_k16_k12k16': 'log10', 'a_k5k12_k5k8k12': 'log10', 'a_k12k16_k8k12k16': 'log10', 'a_k8k12k16_4ac': 'log10', 'a_basal': 'log10', 'noiseParameter1_observable_0ac': 'log10', 'noiseParameter1_observable_4ac': 'log10', 'noiseParameter1_observable_k12': 'log10', 'noiseParameter1_observable_k12k16': 'log10', 'noiseParameter1_observable_k16': 'log10', 'noiseParameter1_observable_k5': 'log10', 'noiseParameter1_observable_k5k12': 'log10', 'noiseParameter1_observable_k5k12k16': 'log10', 'noiseParameter1_observable_k5k16': 'lin', 'noiseParameter1_observable_k5k8': 'log10', 'noiseParameter1_observable_k5k8k12': 'log10', 'noiseParameter1_observable_k5k8k16': 'log10', 'noiseParameter1_observable_k8': 'log10', 'noiseParameter1_observable_k8k12': 'log10', 'noiseParameter1_observable_k8k12k16': 'log10', 'noiseParameter1_observable_k8k16': 'log10'})
2026-09-03 09:12:32.169 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:12:32.169 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'d': np.float64(0.0)}
2026-09-03 09:12:32.169 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:12:32.170 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}
2026-09-03 09:12:32.171 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}
Status: ['AMICI_SUCCESS']
[20]:
# Remove conserved quantities - this requires re-importing the model
# this is enabled by the `AMICI_EXPERIMENTAL_SBML_NONCONST_CLS` environment variable
os.environ["AMICI_EXPERIMENTAL_SBML_NONCONST_CLS"] = "1"
amici_model = import_petab_problem(
petab_problem,
verbose=False,
# we need a different model name if we import the model again
# we cannot load a model with the same name as an already loaded model
model_name="Blasi_CellSystems2016_2",
compile_=True,
)
del os.environ["AMICI_EXPERIMENTAL_SBML_NONCONST_CLS"]
amici_solver = amici_model.create_solver()
amici_solver.set_sensitivity_method(SensitivityMethod.forward)
amici_solver.set_sensitivity_order(SensitivityOrder.first)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
assert all(rdata.status == AMICI_SUCCESS for rdata in res[RDATAS])
2026-09-03 09:12:51.468 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({}, {'d': np.float64(0.0), 'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}, {}, {'d': 'log10', 'a_k8': 'log10', 'a_k5_k5k12': 'log10', 'a_k12_k5k12': 'log10', 'a_k16_k12k16': 'log10', 'a_k5k12_k5k8k12': 'log10', 'a_k12k16_k8k12k16': 'log10', 'a_k8k12k16_4ac': 'log10', 'a_basal': 'log10', 'noiseParameter1_observable_0ac': 'log10', 'noiseParameter1_observable_4ac': 'log10', 'noiseParameter1_observable_k12': 'log10', 'noiseParameter1_observable_k12k16': 'log10', 'noiseParameter1_observable_k16': 'log10', 'noiseParameter1_observable_k5': 'log10', 'noiseParameter1_observable_k5k12': 'log10', 'noiseParameter1_observable_k5k12k16': 'log10', 'noiseParameter1_observable_k5k16': 'lin', 'noiseParameter1_observable_k5k8': 'log10', 'noiseParameter1_observable_k5k8k12': 'log10', 'noiseParameter1_observable_k5k8k16': 'log10', 'noiseParameter1_observable_k8': 'log10', 'noiseParameter1_observable_k8k12': 'log10', 'noiseParameter1_observable_k8k12k16': 'log10', 'noiseParameter1_observable_k8k16': 'log10'})
2026-09-03 09:12:51.469 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {}
2026-09-03 09:12:51.470 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'d': np.float64(0.0)}
2026-09-03 09:12:51.470 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {}
2026-09-03 09:12:51.471 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}
2026-09-03 09:12:51.471 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'a_k8': 'a_k8', 'a_k5_k5k12': 'a_k5_k5k12', 'a_k12_k5k12': 'a_k12_k5k12', 'a_k16_k12k16': 'a_k16_k12k16', 'a_k5k12_k5k8k12': 'a_k5k12_k5k8k12', 'a_k12k16_k8k12k16': 'a_k12k16_k8k12k16', 'a_k8k12k16_4ac': 'a_k8k12k16_4ac', 'a_basal': 'a_basal', 'noiseParameter1_observable_0ac': 'sigma', 'noiseParameter1_observable_4ac': 'sigma', 'noiseParameter1_observable_k12': 'sigma', 'noiseParameter1_observable_k12k16': 'sigma', 'noiseParameter1_observable_k16': 'sigma', 'noiseParameter1_observable_k5': 'sigma', 'noiseParameter1_observable_k5k12': 'sigma', 'noiseParameter1_observable_k5k12k16': 'sigma', 'noiseParameter1_observable_k5k16': nan, 'noiseParameter1_observable_k5k8': 'sigma', 'noiseParameter1_observable_k5k8k12': 'sigma', 'noiseParameter1_observable_k5k8k16': 'sigma', 'noiseParameter1_observable_k8': 'sigma', 'noiseParameter1_observable_k8k12': 'sigma', 'noiseParameter1_observable_k8k12k16': 'sigma', 'noiseParameter1_observable_k8k16': 'sigma'}
Status: ['AMICI_SUCCESS']
Steady state computation failed
Let’s run a simulation:
[21]:
petab_problem = benchmark_models_petab.get_problem("Brannmark_JBC2010")
amici_model = import_petab_problem(
petab_problem,
verbose=False,
)
amici_solver = amici_model.create_solver()
np.random.seed(1851)
problem_parameters = dict(
zip(
petab_problem.x_free_ids,
petab_problem.sample_parameter_startpoints(n_starts=1)[0],
)
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"Status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
# hard to reproduce on GHA
if os.getenv("GITHUB_ACTIONS") is None:
assert [
simulation_status_to_str(rdata.status) for rdata in res[RDATAS]
] == [
"AMICI_ERROR",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
]
2026-09-03 09:13:09.058 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.059 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.060 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.061 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.063 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.063 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.065 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.065 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.067 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.067 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.068 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.068 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.069 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.069 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.070 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.070 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.071 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.071 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.072 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.073 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.073 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.074 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.074 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.075 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.075 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.076 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.076 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.077 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.077 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.078 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.078 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.079 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.080 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.080 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.080 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.081 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.082 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.082 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.083 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.083 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.084 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.084 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.085 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'})
2026-09-03 09:13:09.086 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.087 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8}
2026-09-03 09:13:09.087 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.088 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.088 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.157 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][cvodes:cvHandleFailure:ERR_FAILURE] At t = 736.713 and h = 0.000145837, the error test failed repeatedly or with |h| = hmin.
2026-09-03 09:13:09.158 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][OTHER] AMICI equilibration failed at t=736.713.
2026-09-03 09:13:09.158 - amici.sim.sundials._swig_wrappers - ERROR - [Dose_0+Dose_0][OTHER] AMICI simulation failed: Steady state computation failed. Simulation to steady state failed.
Status: ['AMICI_ERROR', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN']
What happened?
All given experimental conditions require pre-equilibration, i.e., finding a steady state. AMICI first tries to find a steady state using the Newton solver, if that fails, it tries simulating until steady state, if that also fails, it tries the Newton solver from the end of the simulation. In this case, all three failed. Neither Newton’s method nor simulation yielded a steady state satisfying the required tolerances.
This can also be seen in ReturnDataView.preeq_status (the three statuses corresponds to Newton #1, Simulation, Newton #2):
[22]:
rdata = res[RDATAS][0]
rdata.preeq_status
[22]:
[<SteadyStateStatus.not_run: 0>,
<SteadyStateStatus.failed: -1>,
<SteadyStateStatus.not_run: 0>]
How to address?
There are several ways to address that:
Stricter integration tolerances (preferred if affordable - higher accuracy, but generally slower)
Looser steady-state tolerances (lower accuracy, generally faster)
Increase the number of allowed steps for Newton’s method
Let’s try all of them:
[23]:
# Reduce relative tolerance for integration
amici_solver = amici_model.create_solver()
amici_solver.set_relative_tolerance(
1 / 100 * amici_solver.get_relative_tolerance(),
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
rdata = res[RDATAS][0]
print(f"preeq_status={rdata.preeq_status}")
print(f"{rdata.preeq_numsteps=}")
# hard to reproduce on GHA
if os.getenv("GITHUB_ACTIONS") is None:
assert all(rdata.status == AMICI_SUCCESS for rdata in res[RDATAS])
2026-09-03 09:13:09.285 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.286 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.287 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.287 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.289 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.289 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.290 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.290 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.291 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.291 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.292 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.292 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.293 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.294 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.294 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.295 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.295 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.296 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.296 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.297 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.297 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.298 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.298 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.299 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.299 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.300 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.301 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.301 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.302 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.302 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.303 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.304 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.304 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.305 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.305 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.306 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.306 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.307 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.307 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.308 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.308 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.309 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.309 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'})
2026-09-03 09:13:09.310 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.311 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8}
2026-09-03 09:13:09.311 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.312 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.312 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
status: ['AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS']
preeq_status=[<SteadyStateStatus.not_run: 0>, <SteadyStateStatus.success: 1>, <SteadyStateStatus.not_run: 0>]
rdata.preeq_numsteps=array([ 0, 3150, 0])
[24]:
# Increase relative steady state tolerance
for log10_relaxation_factor in range(1, 10):
print(f"Relaxing tolerances by factor {10**log10_relaxation_factor}")
amici_solver = amici_model.create_solver()
amici_solver.set_relative_tolerance_steady_state(
amici_solver.get_relative_tolerance_steady_state()
* 10**log10_relaxation_factor
)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
if all(rdata.status == AMICI_SUCCESS for rdata in res[RDATAS]):
print(
f"-> Succeeded with relative steady state tolerance {amici_solver.get_relative_tolerance_steady_state()}\n"
)
break
else:
print("-> Failed.\n")
print(
"status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
rdata = res[RDATAS][0]
print(f"preeq_status={rdata.preeq_status}")
print(f"{rdata.preeq_numsteps=}")
assert all(rdata.status == AMICI_SUCCESS for rdata in res[RDATAS])
2026-09-03 09:13:09.538 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.539 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.540 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.541 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.542 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.542 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.543 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.543 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.544 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.544 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.545 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.545 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.546 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.547 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.547 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.548 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.548 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.549 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.549 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.550 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.551 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.551 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.551 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.552 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.553 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.553 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.554 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.554 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.555 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.555 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.556 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.557 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.557 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.558 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.558 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.559 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.559 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.560 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.560 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.561 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.561 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.562 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.562 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'})
2026-09-03 09:13:09.563 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.564 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8}
2026-09-03 09:13:09.564 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.565 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.565 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
Relaxing tolerances by factor 10
2026-09-03 09:13:09.642 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][cvodes:cvHandleFailure:ERR_FAILURE] At t = 736.713 and h = 0.000145837, the error test failed repeatedly or with |h| = hmin.
2026-09-03 09:13:09.642 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][OTHER] AMICI equilibration failed at t=736.713.
2026-09-03 09:13:09.644 - amici.sim.sundials._swig_wrappers - ERROR - [Dose_0+Dose_0][OTHER] AMICI simulation failed: Steady state computation failed. Simulation to steady state failed.
2026-09-03 09:13:09.752 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.753 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.754 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.755 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.756 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.757 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.758 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.759 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.760 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.761 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.761 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.762 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.762 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.763 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.764 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.764 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.765 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.765 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.766 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.766 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.767 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.767 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.768 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.768 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.769 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.770 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.770 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.770 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.771 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.771 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.772 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.773 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.773 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.774 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.774 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.775 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.775 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.776 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.776 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.777 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.777 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.778 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.778 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'})
2026-09-03 09:13:09.779 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.779 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8}
2026-09-03 09:13:09.780 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.780 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.781 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
-> Failed.
Relaxing tolerances by factor 100
2026-09-03 09:13:09.852 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][cvodes:cvHandleFailure:ERR_FAILURE] At t = 736.713 and h = 0.000145837, the error test failed repeatedly or with |h| = hmin.
2026-09-03 09:13:09.853 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][OTHER] AMICI equilibration failed at t=736.713.
2026-09-03 09:13:09.854 - amici.sim.sundials._swig_wrappers - ERROR - [Dose_0+Dose_0][OTHER] AMICI simulation failed: Steady state computation failed. Simulation to steady state failed.
2026-09-03 09:13:09.958 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.958 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.960 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.961 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.961 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.962 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.962 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.963 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.963 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.964 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.964 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.965 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.966 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.966 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.967 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.967 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.968 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.968 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.969 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.970 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.970 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.971 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.971 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.972 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.972 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.973 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.973 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.974 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.974 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.975 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.976 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.976 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.977 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.977 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.978 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.978 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.979 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:09.980 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.980 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.981 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.981 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.982 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:09.982 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'})
2026-09-03 09:13:09.983 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:09.983 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8}
2026-09-03 09:13:09.984 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.984 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:09.985 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:10.055 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][cvodes:cvHandleFailure:ERR_FAILURE] At t = 736.713 and h = 0.000145837, the error test failed repeatedly or with |h| = hmin.
2026-09-03 09:13:10.056 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][OTHER] AMICI equilibration failed at t=736.713.
2026-09-03 09:13:10.057 - amici.sim.sundials._swig_wrappers - ERROR - [Dose_0+Dose_0][OTHER] AMICI simulation failed: Steady state computation failed. Simulation to steady state failed.
-> Failed.
Relaxing tolerances by factor 1000
2026-09-03 09:13:10.163 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.164 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.165 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.166 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.166 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.167 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.168 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.168 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.169 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.169 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.170 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.170 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.171 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.172 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.174 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.174 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.175 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.175 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.176 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.177 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.177 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.178 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.178 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.179 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.180 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.181 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.181 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.182 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.182 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.183 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.183 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.184 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.185 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.185 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.186 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.186 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.187 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.188 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.188 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.189 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.189 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.190 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.191 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'})
2026-09-03 09:13:10.191 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.192 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8}
2026-09-03 09:13:10.193 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:10.193 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:10.194 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
-> Failed.
Relaxing tolerances by factor 10000
-> Succeeded with relative steady state tolerance 0.01
status: ['AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS', 'AMICI_SUCCESS']
preeq_status=[<SteadyStateStatus.not_run: 0>, <SteadyStateStatus.success: 1>, <SteadyStateStatus.not_run: 0>]
rdata.preeq_numsteps=array([ 0, 577, 0])
That fixed the error, and took only a quarter of the number steps as the previous run, but at the cost of much lower accuracy.
[25]:
# Let's try increasing the number of Newton steps
# (this is 0 by default, so the Newton solver wasn't used before,
# as can be seen from the 0 in `rdata.preeq_numsteps[0]`)
amici_solver = amici_model.create_solver()
amici_solver.set_newton_max_steps(10**4)
res = simulate_petab(
petab_problem=petab_problem,
amici_model=amici_model,
problem_parameters=problem_parameters,
scaled_parameters=True,
solver=amici_solver,
)
print(
"status:",
[simulation_status_to_str(rdata.status) for rdata in res[RDATAS]],
)
rdata = res[RDATAS][0]
print(f"preeq_status={rdata.preeq_status}")
print(f"{rdata.preeq_numsteps=}")
# hard to reproduce on GHA
if os.getenv("GITHUB_ACTIONS") is None:
assert [
simulation_status_to_str(rdata.status) for rdata in res[RDATAS]
] == [
"AMICI_ERROR",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
"AMICI_NOT_RUN",
]
2026-09-03 09:13:10.392 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.393 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.394 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.395 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.395 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.396 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.396 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.397 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.398 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.01, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.398 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.399 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.399 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.400 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.401 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.401 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.1, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.402 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.402 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.403 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.403 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.404 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.405 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.3, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.405 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.406 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.406 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.407 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.408 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.408 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 10.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.409 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.409 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.410 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.410 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'log10', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'log10', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.411 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.411 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 100.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.412 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.412 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.413 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': 'k_IRP_1Step', 'observableParameter1_IRS1_P': 'k_IRSiP_1Step', 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': 'sigmaY1TimR', 'noiseParameter1_IRS1_P': 'sigmaY2TimR', 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.413 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'lin', 'observableParameter1_IRS1_P_DosR': 'log10', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'lin', 'noiseParameter1_IRS1_P_DosR': 'log10'})
2026-09-03 09:13:10.414 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.415 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 1.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.415 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.415 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.416 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': nan, 'observableParameter1_IRS1_P_DosR': 'k_IRSiP_DosR', 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': nan, 'noiseParameter1_IRS1_P_DosR': 'sigmaYDosR'}
2026-09-03 09:13:10.417 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - PEtab mapping: ({'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8, 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'}, {'k1a': 'log10', 'k1aBasic': 'log10', 'k1b': 'log10', 'k1c': 'log10', 'k1d': 'log10', 'k1e': 'log10', 'k1f': 'log10', 'k1g': 'log10', 'k1r': 'log10', 'k21': 'log10', 'k22': 'log10', 'k3': 'log10', 'k_IRSiP_DosR': 'log10', 'km2': 'log10', 'km3': 'log10', 'insulin_time_1': 'lin', 'insulin_time_2': 'lin', 'insulin_dose_1': 'lin', 'insulin_dose_2': 'lin', 'observableParameter1_IR1_P': 'lin', 'observableParameter1_IRS1_P': 'log10', 'observableParameter1_IRS1_P_DosR': 'lin', 'noiseParameter1_IR1_P': 'lin', 'noiseParameter1_IRS1_P': 'log10', 'noiseParameter1_IRS1_P_DosR': 'lin'})
2026-09-03 09:13:10.418 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters pre-equilibration: {'insulin_time_1': 0.0, 'insulin_time_2': 0.0, 'insulin_dose_1': 0.0, 'insulin_dose_2': 0.0}
2026-09-03 09:13:10.419 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Fixed parameters simulation: {'insulin_time_1': 0.0, 'insulin_time_2': 4.0, 'insulin_dose_1': 1.2, 'insulin_dose_2': 8.8}
2026-09-03 09:13:10.419 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters pre-equilibration: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:10.420 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Variable parameters simulation: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:10.420 - amici.sim.sundials.petab.v1._parameter_mapping - DEBUG - Merged: {'k1a': 'k1a', 'k1aBasic': 'k1aBasic', 'k1b': 'k1b', 'k1c': 'k1c', 'k1d': 'k1d', 'k1e': 'k1e', 'k1f': 'k1f', 'k1g': 'k1g', 'k1r': 'k1r', 'k21': 'k21', 'k22': 'k22', 'k3': 'k3', 'k_IRSiP_DosR': 'k_IRSiP_DosR', 'km2': 'km2', 'km3': 'km3', 'observableParameter1_IR1_P': nan, 'observableParameter1_IRS1_P': 'k_IRSiP_2Step', 'observableParameter1_IRS1_P_DosR': nan, 'noiseParameter1_IR1_P': nan, 'noiseParameter1_IRS1_P': 'sigmaY2Step', 'noiseParameter1_IRS1_P_DosR': nan}
2026-09-03 09:13:10.739 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][cvodes:cvHandleFailure:ERR_FAILURE] At t = 736.713 and h = 0.000145837, the error test failed repeatedly or with |h| = hmin.
2026-09-03 09:13:10.740 - amici.sim.sundials._swig_wrappers - DEBUG - [Dose_0+Dose_0][OTHER] AMICI equilibration failed at t=736.713.
2026-09-03 09:13:10.741 - amici.sim.sundials._swig_wrappers - ERROR - [Dose_0+Dose_0][OTHER] AMICI simulation failed: Steady state computation failed. Simulation to steady state failed.
status: ['AMICI_ERROR', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN', 'AMICI_NOT_RUN']
preeq_status=[<SteadyStateStatus.not_run: 0>, <SteadyStateStatus.failed: -1>, <SteadyStateStatus.not_run: 0>]
rdata.preeq_numsteps=array([ 0, 1105, 0])
Increasing the maximum number of Newton steps doesn’t seem to help here. The Jacobian was numerically singular and its factorization failed. This can be a result of conserved quantities in the model. Section Steady state sensitivity computation failed due to unsuccessful factorization of RHS Jacobian shows how to address that.