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From "Buharov Alexander (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (MATH-1108) SimplexSolver returns TooManyIterationsException
Date Wed, 05 Mar 2014 10:07:43 GMT

    [ https://issues.apache.org/jira/browse/MATH-1108?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13920708#comment-13920708
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Buharov Alexander commented on MATH-1108:
-----------------------------------------

This problem is related with systems biology. This models are saved in SBML-format. And there
are special Matlab TOOLBOX (COBRA) for solving this problem (http://opencobra.sourceforge.net/openCOBRA/Welcome.html).

If you want to test this toolbox. I attached file AdipocyteModel.xml with model (this model
have same non-bounds constraints and object function like previous example). You can instal
COBRA toolbox and make next calculation in Matlab:

model = readCbModel('AdipocyteModel.xml');        % read model
changeCobraSolver('glpk');                                        % choose solver
FBAsolution = optimizeCbModel(model,'max');       % solve

As I understand this solver use modification of simplex method (But I could be wrong). Calculation
time is around 1s. 

> SimplexSolver returns TooManyIterationsException
> ------------------------------------------------
>
>                 Key: MATH-1108
>                 URL: https://issues.apache.org/jira/browse/MATH-1108
>             Project: Commons Math
>          Issue Type: Bug
>    Affects Versions: 3.2, 3.1.1
>            Reporter: Buharov Alexander
>         Attachments: AdipocyteModel.xml, Problem.zip
>
>
> We have vector v and matrix s (from file S.txt)
> v - vector ( size: 1*649 )
> s - matrix ( size: 554*649 )
> We want solve linear problem:
>          *     max (v[31])
>          *     Bounds:
>          *          s*v = 0
>          *          -1 <= v[i] <= 1 for i=0,..., 648 
> We changed  MaxIter parameter (from 100 to 1e+6). And we changed epsilon ( set default
value and 1e-3).  But solver always throws TooManyIterationsException (and work very slow).



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