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NBISweden / workshop_omics_integration

Workshop in omics integration and systems biology
https://nbisweden.github.io/workshop_omics_integration/
GNU General Public License v3.0
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GEMs session lab #41

Open rasools opened 1 month ago

rasools commented 1 month ago

GEMs session lab, not all the notebooks run properly, we need to check them and fix them.

jenfransson commented 2 days ago

I've looked through the labs and there are some problems with packages etc, but a reoccurring issue is whenever model.optimize() is called (in labs 1, 2 and 7), the following error occurs:

SolverError: CPLEX Error 1016: Community Edition. Problem size limits exceeded. Purchase at http://ibm.biz/error1016.

Has this been a problem before? Do we know of a way to fix this? (I have tried it on my local machine as well and get the same error.)

rasools commented 2 days ago

Hi @jenfransson , thanks for looking into this. I am also on it now, but forgot to put my name. The issue is that the size of problem is bigger than the size that free version of CPLEX can handle. One solution could be we use another solver like glpk. I am trying this now to see how it can address the problem.