Installing and switching to Gurobi (COBRApy)

[Stephen Chapman]

Hi all,  

I want to re-create some previous FBA results, but this time I'm using Python and want to choose the same solver, which is the GUROBI solver.  I'm really new to python and struggling to switch solvers from GLPK .

When I type:

>>> m.solver

<optlang.glpk_interface.Model object at 0x114e81c50>

>>> from optlang import gurobi_interface

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/Users/stephenchapman/anaconda/lib/python3.6/site-packages/optlang/gurobi_interface.py", line 36, in <module>

    import gurobipy

ModuleNotFoundError: No module named 'gurobipy'

Now I have downloaded GUROBI and obtained my license, so any help would be greatly appreciated.

Cheers!

[Daniel Espinoza]

Hi Stephen,

From the message, it looks like you have not installed gurobi for python. I would recommend following these directions:

http://www.gurobi.com/documentation/7.5/quickstart_linux/installing_the_anaconda_py.html

Also, if you are switching, I would recommend taking a look at Gurobi's python interface, which is described here

http://www.gurobi.com/documentation/7.5/quickstart_linux/py_python_interface.html

and code examples here

http://www.gurobi.com/documentation/7.5/examples/python_examples.html

Best,

Daniel

[Amarjeet Kumar]

Hello Daniel,

I am able to import gurobipy, optlang in python and also able to import gurobi_interface form optlang
but while performing Flux balance analysis using Cobrapy when I read my model the model does not have any attribute named solver.

Pleas suggest the suitable solution to this problem
Thanks

[Daniel Espinoza]

Hi Amarjeet,

Can you provide a log showing the error? Also, I don't understand what you mean by a model not having a solver attribute... gurobi models don't have such an attribute... could you share a minimal code exhibiting the issue?

Best,

Daniel

[Amarjeet Kumar]

Hi Daniel,

Thanks for the giving me some time. There was a problem with the COBRApy version. I was using very old version of this software. I upgraded it and it was solved.

Thanks for the help.

Thank you

--

---
You received this message because you are subscribed to the Google Groups "Gurobi Optimization" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gurobi+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Best Regards

Amarjeet Kumar

Ph.D. Student

SC&IS, JNU

[Daniel Espinoza]

Glad to hear that,

Best,

Daniel