Multi-thread on OptimizeCbModel

[Magdalena R]

Hello,

I have to analyze a big number of cases with OptimizeCbModel, and to reduce time I was trying to parallel one of the steps. 

I read that the optimization of a linear problem cannot be done in a multi thread, so I was trying with a parallel for (parfor command, MATLAB). However, when running my code I am getting the following error :

Error using solveCobraLP (line 103)
No solver found.  call changeCobraSolver(solverName)
Error in optimizeCbModel (line 159)
solution = solveCobraLP(LPproblem);

I have installed gurobi5 and this problem does not present when running the same code with a normal for. Any idea of why could this be happening? My code is basically this:

range=0:0.1:1;

alpha=1;

ErrorRef=1000;

parfor t=1:length(range)

            beta=range(t);

            maux=NewModel;

            gamma=1-alpha-beta;

            maux=changeObjective(maux,maux.rxns(posBiom),[alpha beta gamma]);

            pesos=zeros((2*5*5),3);

            error=zeros((2*5*5),1);

            u=0;

            for j=0.1:0.1:0.2

                for k=0.1:0.1:0.5

                    for l=0.1:0.1:0.5

                        u=u+1;

                        maux=changeRxnBounds(NewModel,NewModel.rxns(posmATP(1)),j,'b');

                        maux=changeRxnBounds(maux,NewModel.rxns(posmATP(2)),k,'b');

                        maux=changeRxnBounds(maux,NewModel.rxns(posmATP(3)),l,'b');

         

                        pesos(u,:)=[alpha beta gamma];

                        f=optimizeCbModel(maux);

                        error(u)=sum((100*abs(f.x(posBiom))-datos(:,end))./datos(:,end));

                            

                    end

                end

            end

end

        

     

for e=1:length(error)

    if error(e)<ErrorRef

                ErrorRef=error(e);

                alphaOpt=alpha;

                betaOpt=beta;

    end

end

[Almut Heinken]

Dear Magdalena,

just to make sure: did you run changeCobraSolver to set the solver to gurobi before executing this script?

Best

Almut

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[Laurent Heirendt]

Hi Magdalena,

This is an issue with MATLAB that global variables are not properly set during a parfor loop. You can get around this as described here:

https://github.com/opencobra/cobratoolbox/blob/master/.github/guides/FAQ.md#parallel-programming

Please let me know if this helps.

Best,

Laurent

[Magdalena R]

Hi Almut,

I set the Solver to gurobi, and then verified it by running the algorithm in a normal for loop, and it seems to be working. 

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[Magdalena R]

I did what is described in github and now it works, thanks Laurent! 

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