Install/Test All Problems

2012-06-11
2013-05-30
  • Hi, I am a graduate student trying to use a model from the BioModels Database.  The model author told me that they used Cobra so I am switching from just using SBML toolbox and SBToolbox 2. 

    I am currently installing all these programs onto Mac OS 10.7 with Xcode 4.3.2. If necessary I will explore installing all these programs onto a linux supercomputer if the calculations are demanding.

    I have libsbml 5.4.1 compiled and installed with path added to the libraries. 

    I have SBML toolbox 4.1.0 also installed with no errors with added path.   

    I downloaded Gurobi Mex 1.4.5 and have added the path to that.

    I have downloaded Gurobi500 but since I may want to license the supercomputer and the Mac I haven’t installed it yet. 

    With just Gurobi Mex and Cobra, initCobraToolbox returns:
    LP solver set to gurobi successful
    MILP solver set to gurobi successful
    QP solver set to gurobi successful
    MIQP solver set to gurobi successful
    CB map output set to svg successful

    When I run testAll:
    Tests passed:
    testBuildMPS
    testElementalBalance
    testModelManipulation
    testSBML

    Tests not passed:
    testC13Fitting
    testDeletionStudy
    testFBA
    testFVA
    testGDLS
    testGrowthExpMatch
    testMOMA
    testMaps
    testOptKnock
    testRobustnessAnalysis
    testSampleCbModel
    testgpSampler
    testSolvers
    testTissueModel

    Does Gurobi500 need to be installed to pass more tests? What is the functionality without Tomlab?

    Will I need to use the supercomputer or will everything run well on my Mac (2.7 GHz i5 with 8 GB 1333MHz Memory)?

    Also, I’ve been exploring the protocol, but are there any other tutorials out there?

    Thanks!

     
  • Forgot to say I'm using MATLAB 2011B.

     
  • Daniel Hyduke
    Daniel Hyduke
    2012-06-11

    Basically, you need to compile gurobi_mex after downloading it - I believe that the maintainer only provides a binary for 32-bit windows.  Gurobi 5 comes with matlab support so it might not be necessary to use gurobi_mex in the future; I'll be posting a patch soon for gurobi5 for cobra 2.0 and if it works then I'll post a new download in about a week.

    After preliminary testing, the patch will be posted in the patch tracker (https://sourceforge.net/tracker/?group_id=350855&atid=1466444).

    If you want to try using gurobi5 through gurobi_mex you must compile it.
    In the gurobi_mex directory, you'll enter something like the following (based on where your matlab mex binary is and where your gurobi installed itself).

    mex -O -I/Library/gurobi500/mac64/include gurobi_mex.c -L/Library/gurobi500/mac64/lib/ -lgurobi50 -lut -largeArrayDims

    I'd worry about getting through the protocol (excluding c13 analysis) before worrying about supercomputers.

     
  • Thanks for your help!

    The only tests not passed are:
    testC13Fitting
    testSolvers

    Thanks again!

     
  • Huili Yuan
    Huili Yuan
    2013-02-12

    Hi,  I'm starting to use Cobra.  I have Cobra 2.0.5, SBML 4.1.0, and libSBML 5.6.0. I have downloaded gurobi 5.0.2. I 'm using Matlab R2012a. My system is Win7 (64 bit). When doing the testAll() , I can only pass 9 out of 19  tests. I don't know what the problem is, could you give me some help? Thanks in advance!
    PS: Bellow is the complete report concerning testAll().
    >>  initCobraToolbox
    LP solver set to gurobi5 successful
    MILP solver set to gurobi5 successful
    QP solver set to gurobi5 successful
    MIQP solver set to gurobi5 successful
    CB map output set to svg successful
    >> testAll
    Tests passed:
    testBuildMPS
    testElementalBalance
    testGDLS
    testGrowthExpMatch
    testMOMA
    testModelManipulation
    testSBML
    testgpSampler
    testTissueModel

    Tests not passed:
    testC13Fitting
    testDeletionStudy
    testFBA
    testFVA
    testMaps
    testOptKnock
    testRobustnessAnalysis
    testSampleCbModel
    testSolvers
    testpFBA

     
  • Daniel Hyduke
    Daniel Hyduke
    2013-02-13

    Are you using a full commercial, academic, or trial license for Gurobi?  I think that this problem was encountered by somebody before and it was due to the trial license not allowing users to solver larger linear programs.

     
  • Huili Yuan
    Huili Yuan
    2013-02-13

    Yes, I got a free academic license. In your opinion, it's the problem of gurobi?

     
  • Huili Yuan
    Huili Yuan
    2013-02-13

    By the way, I'm a new user to both Cobra and Matlab. Although I read some papers related to cobra or FBA, but I don't know how to operate it in matlab. Do you have good suggestions for my case? Thanks!

     
  • Daniel Hyduke
    Daniel Hyduke
    2013-02-13

    Did you make sure that your gurobi license was active, don't know how it works on windows but on macs you have to do something like grbvalidate? (The matlab version only checks if gurobi is installed not if it it functions)

    Run testFVA() after initCobraToolbox and send me the output.

    Or you can try the python version if you've got experience with python.

     
  • Huili Yuan
    Huili Yuan
    2013-02-13

    Thanks a lot! I have  solved  the problem already. It's not the problem of gurobi.
    By the way, after running testFVA(), the output is:
    >>testFVA
    Error using cd
    Too many input arguments.

    Error in testFVA (line 10)
    cd(test_folder.path);

    PS: Errors in cd and findRxnIDs