Large model Solver/Simulator construction errors in Python 3

[bgyori]

When trying to simulate models above a certain size (this is vague, but see example below) in Python 3, I get the following error:

In [10]: sim = ScipyOdeSimulator(model, numpy.linspace(0, 100))
Traceback (most recent call last):
  File "/Users/ben/.virtualenvs/py36/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2910, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-10-2af18e3a9d87>", line 1, in <module>
    sim = ScipyOdeSimulator(model, numpy.linspace(0, 100))
  File "/Users/ben/.virtualenvs/py36/lib/python3.6/site-packages/pysb/simulator/scipyode.py", line 183, in __init__
    sympy.flatten(ode_mat))
  File "/Users/ben/.virtualenvs/py36/lib/python3.6/site-packages/sympy/utilities/lambdify.py", line 434, in lambdify
    func = eval(lstr, namespace)
  File "<string>", line 1
SyntaxError: more than 255 arguments

I tried this in Python 3.5 and 3.6, and tried with both git cloned and setup.py installed PySB, and pip installed PySB (1.5.0). I tried both pysb.integrate.Solver and pysb.simulator.ScipyOdeSimulator. All result in the same error. I also tried the same in Python 2 and it worked.

To not make things more complicated with a real model, I experimented a bit with auto-generated models. I generated a model in which monomers named A-Z pairwise phosphorylate each other. I found that the error went away when I only had monomers A-T, and first appeared when I had monomer U in the model - this is the model I'm attaching.

from pysb_model import model
from pysb.simulator import ScipyOdeSimulator
sim  = ScipyOdeSimulator(model)

pysb_model.py.zip

[alubbock]

The ScipyOdeSimulator constructor converts your system of ODEs into code for execution, either using the weave library to convert them into C code, or sympy to convert them into Python functions. Until recently, Python had a limit of 255 arguments per function call, which is the limit you're hitting upon above. However, this limit will be removed in Python 3.7.

Your options are:

• Use Python 2.7 with weave installed. This is recommended where possible, as the C code produced by weave will be much faster than Python code.
• Upgrade to a pre-release version Python 3.7 to avoid the 255 argument limit. Not recommended, as PySB hasn't been tested with Python 3.7 yet.
• Try the experimental use_theano=True flag, e.g. ScipyOdeSimulator(model, use_theano=True). Theano compiles your ODEs to C code like weave, so it should also be fast, but it isn't as well tested in PySB yet. This is probably your best option if you want to use Python 3 with ScipyOdeSimulator.
• Use a different Simulator, e.g. the CupSodaSimulator if you have a compatible NVIDIA GPU available.

[bgyori]

Thanks, that's really informative! I went ahead with the Theano solution and it works well in Python 3. Looks like I missed this option because it's not documented -- perhaps it would be worth mentioning in the ScipeOdeSimulator docstrings (even if it's not very well tested yet).

[alubbock]

Update to this ticket: preferred solution now would be to use ScipyOdeSimulator(model, compiler='cython'). Python 3.7 has also been released, which would also address the problem as described above. I'll close the ticket.