rmtfleming
commented
1 year ago Hi Bastian, is exist('solveCobraLP') == 2 on your machine? It may not be finding an x0 in the polytope due to numerical issues. Are any of your bounds very close together? e.g. ub - lb < 1e-6 ?
Try 'RHMC' as the sampler, that is another option.
Regards,
Ronan
On Mon, 14 Nov 2022 at 12:03, Bastien-N @.***> wrote:
Good afternoon,
I have run into a problem with the chrrSampler, more specifically the rounding part of it. The model I am using is the latest version of the Human1 model ( https://github.com/SysBioChalmers/Human-GEM).
The exact error is: " Error using mve_solver_cobra (line 29) x0 not interior
Error in mve_run_cobra (line 32) [x,E2,converged] = mve_solver_cobra(A,b,x0,maxiter,tol2,reg); %Ben
Error in preprocess (line 255) [T_shift, Tmve,converged] = mve_run_cobra(P.A,P.b, x0,reg);
Error in chrrSampler(line 110) [roundedPolytope] = preprocess(P,options); "
From the tests I was able to do, it seems that somehow the getCCcenter function defined in preprocess does not return a point that is interior to the polytope, but it does not give an error either.
I also have:
- Tried a fresh installation of matlab, gurobi, and cobraToolbox on different hardware. This did not work.
- Tried sampling a different smaller model, which went fine.
I hereby confirm that I have:
- Tried to solve the issue on my own
- Retried to run my code with the latest version of The COBRA Toolbox
- Checked that a similar issue has not already been opened
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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming
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Bastien-N
Good afternoon,
I have run into a problem with the chrrSampler, more specifically the rounding part of it. The model I am using is the latest version of the Human1 model (https://github.com/SysBioChalmers/Human-GEM).
The exact error is: " Error using mve_solver_cobra (line 29) x0 not interior
Error in mve_run_cobra (line 32) [x,E2,converged] = mve_solver_cobra(A,b,x0,maxiter,tol2,reg); %Ben
Error in preprocess (line 255) [T_shift, Tmve,converged] = mve_run_cobra(P.A,P.b, x0,reg);
Error in chrrSampler(line 110) [roundedPolytope] = preprocess(P,options); "
From the tests I was able to do, it seems that somehow the getCCcenter function defined in preprocess does not return a point that is interior to the polytope, but it does not give an error either.
I also have:
I hereby confirm that I have: