Problem in parameter fitting (pravastatin)

[matthiaskoenig]

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/usr/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/usr/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/fit/runner.py", line 176, in worker
    return _run_optimization_serial(**kwargs)  # type: ignore
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/utils.py", line 60, in timed
    result = function(*args, **kw)
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/fit/runner.py", line 236, in _run_optimization_serial
    fits, trajectories = problem.optimize(
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/fit/optimization.py", line 561, in optimize
    fit, trajectory = self._optimize_single(
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/utils.py", line 60, in timed
    result = function(*args, **kw)
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/fit/optimization.py", line 608, in _optimize_single
    opt_result = scipy.optimize.least_squares(
  File "/home/mkoenig/.virtualenvs/pkdb_models/lib/python3.9/site-packages/scipy/optimize/_lsq/least_squares.py", line 928, in least_squares
    result = trf(fun_wrapped, jac_wrapped, x0, f0, J0, lb, ub, ftol, xtol,
  File "/home/mkoenig/.virtualenvs/pkdb_models/lib/python3.9/site-packages/scipy/optimize/_lsq/trf.py", line 123, in trf
    return trf_bounds(
  File "/home/mkoenig/.virtualenvs/pkdb_models/lib/python3.9/site-packages/scipy/optimize/_lsq/trf.py", line 338, in trf_bounds
    f_new = fun(x_new)
  File "/home/mkoenig/.virtualenvs/pkdb_models/lib/python3.9/site-packages/scipy/optimize/_lsq/least_squares.py", line 815, in fun_wrapped
    return np.atleast_1d(fun(x, *args, **kwargs))
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/fit/optimization.py", line 686, in residuals
    simulator.set_model(model=self.models[k])
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/simulator/simulation_serial.py", line 54, in set_model
    self.model = RoadrunnerSBMLModel(
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/model/model_roadrunner.py", line 90, in __init__
    self.uinfo = self.parse_units(ureg)
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/model/model_roadrunner.py", line 182, in parse_units
    uinfo = UnitsInformation.from_sbml(sbml=self.source.path, ureg=ureg)
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/units.py", line 91, in from_sbml
    return UnitsInformation.from_sbml_doc(doc, ureg=ureg)
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/units.py", line 197, in from_sbml_doc
    uid_dict: Dict[str, str] = UnitsInformation.model_uid_dict(model, ureg=ureg)
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/units.py", line 157, in model_uid_dict
    for udef in model.getListOfUnitDefinitions():
AttributeError: 'NoneType' object has no attribute 'getListOfUnitDefinitions'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/mkoenig/git/pkdb_models/pkdb_models/models/pravastatin/fitting/fitting.py", line 257, in <module>
    results = run_fit_subset(
  File "/home/mkoenig/git/pkdb_models/pkdb_models/models/pravastatin/fitting/fitting.py", line 209, in run_fit_subset
    results_all: Dict[str, Tuple[OptimizationResult, OptimizationProblem]] = fit_pravastatin(
  File "/home/mkoenig/git/pkdb_models/pkdb_models/models/pravastatin/fitting/fitting.py", line 159, in fit_pravastatin
    results[opid] = fit_op(op)
  File "/home/mkoenig/git/pkdb_models/pkdb_models/models/pravastatin/fitting/fitting.py", line 134, in fit_op
    opt_result, op = fitlsq(op, size=10, n_cores=10, **fit_kwargs)
  File "/home/mkoenig/git/pkdb_models/pkdb_models/models/pravastatin/fitting/fitting.py", line 60, in fitlsq
    opt_res = run_optimization(
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/utils.py", line 60, in timed
    result = function(*args, **kw)
  File "/home/mkoenig/git/sbmlsim/src/sbmlsim/fit/runner.py", line 159, in run_optimization
    opt_results: List[OptimizationResult] = pool.map(worker, args_list)
  File "/usr/lib/python3.9/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/usr/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
AttributeError: 'NoneType' object has no attribute 'getListOfUnitDefinitions'