Problem installing cobra toolbox

[Qausar]

Dear all, 

I'm trying to install cobra toolbox on my PC:

Windows 10

Matlab 2013b

Gurobi 6.5.0

I followed the guidelines from this link http://benheavner.com/systemsbio/index.php?title=COBRA_on_Matlab_64

However, at compiler setting, for choosing compiler, the Matlab didn't detect the compiler available although I have installed the Visual C++. The error I got:

>> mex -setup

 

Welcome to mex -setup.  This utility will help you set up  

a default compiler.  For a list of supported compilers, see  

http://www.mathworks.com/support/compilers/R2013b/win64.html 

 

Please choose your compiler for building MEX-files: 

 

Would you like mex to locate installed compilers [y]/n? y

 

No supported SDK or compiler was found on this computer. 

For a list of supported compilers, see  

http://www.mathworks.com/support/compilers/R2013b/win64.html  

 

Unable to complete successfully.

Currently, I'm not sure whether the problem is non-compatible with the Windows 10 or the MSVC I've downloaded is not supported for Windows 10.

Please help.

Thank you.

[Ronan M.T. Fleming]

Hi
Those instructions are out of date. Clone the latest code from the git repo. Get Gurobi 650 as no mex -setup required plus libsbml is also packaged with cobra toolbox now and should work fine.
Regards
Ronan

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[Qausar]

Thank you Ronan.

The git repo, refer to this: https://opencobra.github.io/cobratoolbox/ ? 

Is there any guidelines that I can follow to install the cobra? 

Thank you.

[Ronan M.T. Fleming]

Hi,

for a windows user, this is how I imaging the steps:

1. Install gurobi 6.*
http://www.gurobi.com/documentation/

including "Setting up Gurobi for MATLAB"

2. Install github desktop
https://help.github.com/desktop/guides/getting-started/setting-up-github-desktop/

3. Clone the git cobratoolbox repository, using this url: https://github.com/opencobra/cobratoolbox.git
https://help.github.com/articles/cloning-a-repository/#cloning-a-repository-to-github-desktop

4. In matlab, navigate to yourpath/cobratoolbox/external then run the following command in the matlab command line
addpath_recurse('~/work/code/cobratoolbox',{'obsolete','m2html','docs'});

4. In matlab, run the command
initCobraToolbox()

Then you should a message like this:

>> initCobraToolbox
Define LP solver...
LP solver: gurobi6

Define MILP solver...
MILP solver: gurobi6

Define QP solver...
QP solver: gurobi6

Define MIQP solver...
MIQP solver: gurobi6

Installing the SBMLToolbox.

* Doing preliminary checks of runtime environment ...
  - This appears to be MATLAB and not Octave.
  - MATLAB reports the OS is 64-bit Linux.

Checking for libSBML MATLAB binding

Document written
libSBML MATLAB binding found and working

Installation successful
TranslateSBML worked with the test .xml file: Ecoli_core_ECOSAL.xml

Regards,

Ronan

 

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[gianluca mattei]

Hi
I had the same problem. Gurobi and W10 seems to be not compatible (for example you'll need .NET framework 4.0 not available for W 10) and it requires some workarounds to use last version of the solver. Try using glpk instead of gurobi, this will save you a lot of time.

[Ronan M.T. Fleming]

Dear Gianluca et al,

please follow this gurobi guide to install:

http://www.gurobi.com/documentation/6.5/quickstart_windows.pdf

I reiterate, there is no need for gurobi_mex any longer. We still keep that interface for backward compatibility, but I don't actually know anyone who still uses it.

Ben,

please remove or update your webpage as it refers to a time before there existed a native matlab interface for gurobi and may be causing confusion out there about how to install solvers interfaced to the COBRA toolbox. Ideally, if you want to write a new readme, then make a pull request and we will add it to the git repo.

http://benheavner.com/systemsbio/index.php?title=COBRA_on_Matlab_64

Regards,

Ronan

--

[Ben]

You bet. I should be able to update that page next week. It is pretty old, for sure. I've long been pleasantly surprised at how useful that particular set of notes has been for the community.

-b

[Qausar]

Hi,

Thanks for the guidelines.

I've installed everything according to the guidelines, however when I'm trying to set up the Gurobi for Matlab, this error occur:

 

Error using gurobi_setup (line 90)

Invalid MEX-file 'C:\Program Files (x86)\gurobi\win64\matlab\gurobi.mexw64': The specified module could not be found.

However, in that directory, the specified module is already there. 

Thank you

[Ronan M.T. Fleming]

Hi Qausar,

this is a problem with how you installed gurobi. They have a google group:

https://groups.google.com/forum/#!forum/gurobi

Someone else reported the same problem I think, and a solution is there:

https://groups.google.com/forum/#!searchin/gurobi/gurobi.mexw64/gurobi/eEKAOif70Z0/_qyA14la4x0J

Regards,

Ronan

[Qausar]

Dear all,

Thank you for your helpfulness, I've successfully installed the COBRA toolbox on my desktop. Thank you very much.

[Huansheng Cao]

Hi there, 

my systems: 64-bit win7, matlab 2014a, cobra cloned from github.

I have done exactly the same thing as Ronan instructed, but only got 12 of 32 tests passed. before I install Gurobi 6.05, I got 15 of 32 tests passed. please help

Tests passed: 

>> initCobraToolbox()

Define LP solver...

LP solver: gurobi6 

Define MILP solver...

MILP solver: gurobi6

Define QP solver...

QP solver: gurobi6

Define MIQP solver...

MIQP solver: gurobi6

Define CB map output...

CB map output: svg

TranslateSBML worked with the test .xml file: Ecoli_core_ECOSAL.xml

>> testAll()

Solver set to MPS. This function will write out a .MPS file and return a matrix string for the LP problem

Solver set to MPS. This function will output an MPS matrix string for the MILP problem

testBuildMPS successfully passed

Error in testC13Fitting

Error in testDeletionStudy

testElementalBalance successfully passed

ans =

     1

Error in testFASTCORE

Error in testFBA

Error in testFVA

|J|=4112  Error in testFastcc

|J|=6  |A|=5

....

....

testBuildMPS

testElementalBalance

testFluxConsistency

testGDLS

testGrowthExpMatch

testMaps

testModelManipulation

modelCitations_update

testRobustnessAnalysis

testSBML

testgpSampler

testSubspaces

Tests not passed: 

testC13Fitting

testDeletionStudy

testFASTCORE

testFBA

testFVA

testFastcc

testMOMA

modelCitations

sbmlTestModelToMat

testModels

testModelsAlgorithmically

testNullspace

testOptKnock

testRank

testSampleCbModel

testDifferentLPSolvers

testSolvers

testStoichiometricConsistency

testTissueModel

testpFBA

IT IS NOT NECESSARY FOR THE COBRA TOOLBOX TO PASS ALL TESTS TO FUNCTION; HOWEVER, IT MUST PASS THE TESTS THAT ARE RELEVANT TO YOUR PARTICULAR PROBLEM!!!

Tests may not pass for several reasons.  Some of the most common issues:

1.  The correct solver is not installed.  Certain tests require LP, MILP, QP or NLP solvers.  See changeCobraSolvers.m for a complete list of supported solvers.

These tests will fail when running testAll unless one has the tomlab suite installed.  If all of the functions that you require for your use function then do not worry about them: testC13Fitting, testGDLS, testMOMA, testOptKnock, testSolvers

If a particular test fails, you can run that test individually for more information

ans =

12 of 32 tests completed successfully.

[Giu Bon]

Hi,
I'm also a noob in here. The same happens to me when using gurobi6 as LP solver for FBA.
Try to use tomlab. It worked fine to me.
Then, in order to save it as your first LP solver, try to open the initCobraToolbox file, look for % Define LP solver
and add tomlab_cplex as your first solver

CobraLPSolver = {'tomlab_cplex', 'cplx', ...}

Or better if you wait for somebody more expert. However, this advice can't be harmful to you pc, so you can try it easy.

Let us know