moma failures

[danielhyduke]

Somewhere in the last set up updates MOMA appears to have stopped functioning.
from cobra.test import create_test_model

model = create_test_model()
from cobra.flux_analysis import single_deletion
single_deletion(model, ['STM0247'], method='moma', solver='gurobi')
single_deletion(model, ['STM0247'], method='moma', solver='gurobi')

cplex 12.5
gurobi 5.5
0.3.0.dev-118-g09707d2
OS X 10.9.1
Python 2.7.5 (default, Aug 25 2013, 00:04:04)
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin

Could somebody confirm that the failure happens on another OS?

[aebrahim]

My output

Python 2.7.3 (default, Sep 26 2013, 20:03:06) 
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from cobra.test import create_test_model
>>> 
>>> model = create_test_model()
>>> from cobra.flux_analysis import single_deletion
>>> single_deletion(model, ['STM0247'], method='moma', solver='gurobi') 
/home/aebrahim/cobrapy/cobra/flux_analysis/moma.py:63: UserWarning: moma currently does not support reusing models or problems. continuing without them
  "continuing without them")
({'STM0247': 0.38000797000000003}, {'STM0247': 'optimal'}, {'STM0247': 'discarded'})
>>> single_deletion(model, ['STM0247'], method='moma', solver='cplex')
/home/aebrahim/cobrapy/cobra/flux_analysis/moma.py:161: UserWarning: optimal moma solution not found: solver status failed returning the problem, the_combined model, and the quadratic component for trouble shooting
  ' returning the problem, the_combined model, and the quadratic component for trouble shooting')
({'STM0247': nan}, {'STM0247': 'failed'}, {'STM0247': 'discarded'})
>>> import cobra; print cobra.__version__
0.3.0.dev-118-g09707d2

[danielhyduke]

Thanks. It looks like it's an issue with cplex. I'll see if I can figure it out.

I didn't have gurobi installed on my test machine so it defaulted to cplex.