ibm_cplex not working

[Akhila George]

Hi,

I installed IBM ILOG CPLEX Optimization studio 12.8 in windows 10. In MATLAB (R2020b), the path is set to cplex\matlab\x64_win64 folder. However, ibm_cplex seems to be not working while running initCobraToolbox. Please see the attached for the details.

Thanks. 

Kind regards,

Akhila

[Ronan M.T. Fleming]

Hi Akhilia,
what is the output from:

solverName = 'ibm_cplex';
solverType = 'LP';
printLevel = 2;
validationLevel = 2;
[solverOK, solverInstalled] = changeCobraSolver(solverName,
solverType, printLevel, validationLevel)

Regards,

Ronan

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[Akhila George]

Hi Ronan,

Please see the following output. Thanks.

solverOK =

  logical

   0

solverInstalled =

  logical

   0

Kind regards,

Akhila

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[Akhila George]

Hi Ronan,

How can I fix this issue?

Thanks.

Kind regards,

Akhila

[Ronan M.T. Fleming]

Hi Akhila,

run

updateCobraToolbox()

then
run

solverName = 'ibm_cplex';
solverType = 'LP';
printLevel = 2;
validationLevel = 2;
[solverOK, solverInstalled] = changeCobraSolver(solverName,
solverType, printLevel, validationLevel)

My output is below:
[solverOK, solverInstalled] = changeCobraSolver(solverName,solverType,
printLevel, validationLevel)

> changeCobraSolver: IBM ILOG CPLEX interface added to MATLAB path.
> ibm_cplex (version 1210) is compatible and fully tested with MATLAB
R2021a on your operating system.
Version identifier: 12.10.0.0 | 2019-11-26 | 843d4de
CPXPARAM_Output_WriteLevel 3
CPXPARAM_Output_CloneLog -1
Found incumbent of value 0.000000 after 0.01 sec. (0.00 ticks)

Root node processing (before b&c):
Real time = 0.01 sec. (0.00 ticks)
Parallel b&c, 8 threads:
Real time = 0.00 sec. (0.00 ticks)
Sync time (average) = 0.00 sec.
Wait time (average) = 0.00 sec.
------------
Total (root+branch&cut) = 0.01 sec. (0.00 ticks)

solverOK =

logical

1


solverInstalled =

logical

1

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[Akhila George]

Hi Ronan,

I came across the following error while running updateCobraToolbox()

Error using cd

Cannot CD to C:\Program Files\MATLAB\R2020b\toolbox\cobratoolbox\.tmp (Name is

nonexistent or not a directory).

Error in portableGitSetup (line 43)

        cd([CBTDIR filesep tmpFolder]);

Error in installGitBash (line 32)

            portableGitSetup(gitBashVersion, 0);

Error in updateGitBash (line 81)

                installGitBash();

Error in updateCobraToolbox (line 20)

        updateGitBash(fetchAndCheckOnly);

How can I fix this?

Kind regards,

Akhila

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[Ronan M.T. Fleming]

Hi Akhila,
reading the code and debugging it. e.g. I see the lines:

% define the name of the temporary folder
tmpFolder = '.tmp';

% create .tmp if not already present
if ~exist(tmpFolder, 'dir')
mkdir(tmpFolder);
end

% determine architecture
archstr = computer('arch');
archBit = archstr(end-1:end);

% save the current directory
currentDir = pwd;

% change to temporary directory

cd([CBTDIR filesep tmpFolder]);

Does the folder exist, are the permissions there to make the folder?
This is an open source project with 250k lines. Try to debug it
yourself and if you find a solution, post it here, or better yet make
the contribution so that it will also be fixed by others. If you are
still stuck, then ask again.
Regards,
Ronan

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[Akhila George]

Hi Ronan,

The updateCobraToolbox() didn't update the CobraToolbox due to unstaged files, it seems. Then I happened to remove the installation for reinstalling CobraToolbox by following the instructions given for removing legacy installation. But now in gitBash, it says the following:

$ git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox

fatal: destination path 'cobratoolbox' already exists and is not an empty directory.

How can I fix this?  How can I reinstall CobraToolbox.

Thanks for your help.

Kind regards,

Akhila

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[Ronan M.T. Fleming]

Hi Akhila,
if you have unstaged files it may mean that you have edited some of
the cobra toolbox or put some files in that folder. In that case
updateCobraToolbox() will not overwrite your local changes. It is only
designed to update if one does not have local changes. You have two
options:
1) if you want to just use the cobra toolbox but not make changes to
it, and discard your existing changes, then delete the existing cobra
toolbox folder and install a new version.
2) if you want use and change files in the cobra toolbox (for sharing
with the community later) you need to go this route:
https://opencobra.github.io/cobratoolbox/latest/contributing.html
After you have a fork-cobratoolbox installation then go into the old
cobratoolbox folder and from the command line use:
git status
That will show you the files you changed that you may wish to move
over into the fork-cobratoolbox version.
Regards,
Ronan

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[Akhila George]

Hi Ronan,

I chose the first option in your mail. Deleted CobraToolbox folder from MATLAB and then cloned the repository again using GitBash. It shows the following error while the current folder is cobratoolbox..

>> initCobraToolbox

Unrecognized function or variable 'initCobraToolbox'.

How shall I fix this? Thanks.

Kind regards,

Akhila

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[Ronan M.T. Fleming]

https://nl.mathworks.com/matlabcentral/answers/96005-why-do-i-get-the-error-undefined-function-or-variable

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[Akhila George]

Thanks, Ronan. I'm able to initialize cobraToolbox by removing custom paths in Matlab. 

Kind regards,

Akhila

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[Akhila George]

Hi Ronan,

I got the following output.

>> updateCobraToolbox()

 > Checking for available updates ...

 > Extracting the gitBash archive (this may take a while) ... Done.

 > gitBash folder (C:\Program Files\MATLAB\R2020b\toolbox\cobratoolbox\.tmp\PortableGit-2.13.3) could not be renamed.

 > gitBash successfully installed.

 > remote.origin.url = https://github.com/opencobra/cobratoolbox.git

.

 > currentBranch = master.

 > The COBRA Toolbox is up-to-date.

>> solverName = 'ibm_cplex';

>> solverType = 'LP';

>> printLevel = 2;

>> validationLevel = 2;

>> [solverOK, solverInstalled] = changeCobraSolver(solverName,solverType, printLevel, validationLevel)

 > changeCobraSolver: IBM ILOG CPLEX interface added to MATLAB path.

 > The solver compatibility is not tested with MATLAB R2020b.

solverOK =

  logical

   0

solverInstalled =

  logical

   0

Kind regards,

Akhila

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[Ronan M.T. Fleming]

Hi Akhila,

I don't know. I don't use windows. Try a different solver. Gurobi?

Could some other windows user help Akhila?

Regards,

Ronan

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[Ronan M.T. Fleming]

put a breakpoint on this line
https://github.com/opencobra/cobratoolbox/blob/531bc415edab4d1b7c0cd9fd78ac867a706cd6ac/src/base/solvers/getSetSolver/changeCobraSolver.m#L514
then debug it

On Mon, 14 Jun 2021 at 01:32, Ronan M.T. Fleming

[Akhila George]

Thanks. Gurobi is working.

Kind regards,

Akhila

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[Johannes van Beek]

I encountered the same problem (one difference: Matlab veriosn 2020a) as Akhila running initCobraToolbox and also running other code which calls changeCobraSolver.m. I noticed the following when trying to find the cause:

when reaching

changeCobraSolver.m line 445 and following :

case {'ibm_cplex','cplexlp'}

            try

                ILOGcplex = Cplex('fba');  % Initialize the CPLEX object

                solverOK = true;

            catch ME

                solverOK = false;

            end

            matver=split(version,'.');

            matver=str2double(strcat(char(matver(1)),'.',char(matver(2))));

            if matver < 8.6

                warning('off', 'MATLAB:lang:badlyScopedReturnValue');  % take out warning message

            end

this generates an exception, which is not reported, but  the  exception is caught and solverOK is set to 'false'. If the call to Cplex is commented out at first glance the installation seems to be OK, but problems arise on further calls to Cplex().

The exception is something like:

K>> ILOGcplex = Cplex('fba')

Error using Cplex

Error:File: Cplex.p Line: 942 Column: 0

Identifier 'changedParam' is not a function or a shared variable. To

share 'changedParam' with nested function, initialize it in the current

scope. For more information, see Sharing Variables Between Parent and

Nested Functions. 

at another occasion:

ME = 

  MException with properties:

    identifier: 'MATLAB:lang:IdentifierNotSharedVariableWithNestedScope'

       message: 'Error:File: Cplex.p Line: 942 Column: 0↵Identifier 'changedParam' is not a function or a shared variable. To share 'changedParam' with nested function, initialize it in the current scope. For more information, see Sharing Variables Between Parent and Nested Functions.'

         cause: {}

         stack: [4×1 struct]

    Correction: []

Cplex.p is a content-obscured, executable file and I do not know how to search further.

The problem arises each time Cplex() is called via initCobraToolbox or during other calls to changeCobraSolver.

At one occasion there was also mention of Cplex not being installed or the IBM license server not being reached.

However,  other calls of Cplex functions in matlab code which does not use the cobratoolbox still work well.

Kind Regards,

Hans van Beek

Op maandag 14 juni 2021 om 04:24:57 UTC+2 schreef akhila...@gmail.com:

[Ronan M.T. Fleming]

Hi Hans,
here is the same error from something unconnected to cplex:
https://www.programmersought.com/article/27296334458/
They have different cplex interfaces, maybe its just the object
oriented one that is problematic?
Regards,
Ronan

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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
&
H2020 Project Coordinator,
Systems Medicine of Mitochondrial Parkinson’s Disease,
http://sysmedpd.eu

[Ronan M.T. Fleming]

Hi Hans,

did you ever find a solution to that issue "Identifier 'changedParam' is not a function or a shared variable."

It has occurred again:

https://github.com/opencobra/cobratoolbox/issues/1861

Regards,

Ronan

[Ronan M.T. Fleming]

Thanks to Tim Hensen @trjhensen for getting to the bottom of this cplex issue. See here:

https://github.com/opencobra/cobratoolbox/issues/1868