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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Problem size limits exceeded with free edition of CPLEX #48

Closed lavik17 closed 5 years ago

lavik17 commented 5 years ago

Running on Carveme on a single genome and still getting an error of Problem size limits exceeded. This is using CPLEX with academic credentials. Is there a solution other than purchasing the commercial license?

cdanielmachado commented 5 years ago

Hi @lavik17

You are using the demo version, which is not exactly the same as academic license.

You need to sign up for an academic license at IBM and download the fully functional version of cplex. This is free for academics, there is no cost.

Sububioinfo commented 4 years ago

Hi am using academic version cplex_studio1210.linux-x86-64.bin Still am getting an error

Sububioinfo commented 4 years ago

This is my error Traceback (most recent call last): File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/bin/carve", line 364, in ref_score=args.reference_score File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/bin/carve", line 198, in main debug_output=debug_output) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/carveme/reconstruction/carving.py", line 236, in carve_model ref_reactions=ref_reactions, ref_score=ref_score, debug_output=debug_output) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/carveme/reconstruction/carving.py", line 123, in minmax_reduction solver.update() File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/framed/solvers/cplex_interface.py", line 206, in update self.add_variables(var_ids, lbs, ubs, vartypes) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/framed/solvers/cplex_interface.py", line 105, in add_variables self.problem.variables.add(names=var_ids, lb=lbs, ub=ubs, types=vartypes) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_subinterfaces.py", line 456, in add obj, lb, ub, types, names, columns) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_baseinterface.py", line 41, in _add_iter addfun(*args, **kwargs) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_subinterfaces.py", line 378, in _add types, names) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_procedural.py", line 967, in newcols xctype, colname) File "/storage/dhome/jsankarasubramani/miniconda3/envs/carveme/lib/python3.6/site-packages/cplex/_internal/_pycplex.py", line 1785, in CPXXnewcols return _pycplex_platform.CPXXnewcols(env, lp, ccnt, py_obj, py_lb, py_ub, xctype, colname) TypeError: not a list

cdanielmachado commented 4 years ago

Please check https://github.com/cdanielmachado/carveme/issues/81