Error in run "testMgPipe"

Joo-Young Lee

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Apr 27, 2020, 6:41:17 PM4/27/20

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Hello,

I hope you all stay healthy and safe. I am new to COBRA Toolbox and have a issue to run "testMgPipe".

I wanted to run MgPipe with AGORA model to analyze trophic web in my 16S amplicon seq data. I installed COBRA Toolbox and IBM ILOG CPLEX (v.12.8) for running on linux environment via university HPCC. After "initCobraToolbox", I found there was a warning. Also, I received errors when I ran "testMgPipe". I have copied and pasted details from matlab command window. Please help me to solve this issue. Thank you for your time and consideration.

Cheers,

Joo-Young

>> initCobraToolbox

_____ _____ _____ _____ _____ |

/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis

| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2020

| | | | | | | _ { | _ / | ___ | |

| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:

\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox

|

> Checking if git is installed ... Done (version: 1.8.3.).

> Checking if the repository is tracked using git ... Done.

> Checking if curl is installed ... Done.

> Checking if remote can be reached ... Done.

> Initializing and updating submodules (this may take a while)... Done.

> Adding all the files of The COBRA Toolbox ... Done.

> Define CB map output... set to svg.

> TranslateSBML is installed and working properly.

> Configuring solver environment variables ...

- [--*-] ILOG_CPLEX_PATH: /mnt/home/leejooy5/ILOG/CPLEX_Studio128/cplex/matlab/x86-64_linux

- [----] GUROBI_PATH: --> set this path manually after installing the solver ( see instructions )

- [----] TOMLAB_PATH: --> set this path manually after installing the solver ( see instructions )

- [----] MOSEK_PATH: --> set this path manually after installing the solver ( see instructions )

Done.

> Checking available solvers and solver interfaces ...Warning: File: Cplex.p Line: 965 Column: 0

Defining "changedParam" in the nested function shares it with the parent function. In a future release, to share

"changedParam" between parent and nested functions, explicitly define it in the parent function.

> In changeCobraSolver (line 435)

In initCobraToolbox (line 405)

Done.

> Setting default solvers ... Done.

> Saving the MATLAB path ... Done.

- The MATLAB path was saved as ~/pathdef.m.

> Summary of available solvers and solver interfaces

Support LP MILP QP MIQP NLP

----------------------------------------------------------------------

gurobi active 0 0 0 0 -

ibm_cplex active 1 1 1 1 -

tomlab_cplex active 0 0 0 0 -

glpk active 1 1 - - -

mosek active 0 - 0 - -

matlab active 1 - - - 1

pdco active 1 - 1 - -

quadMinos active 1 - - - -

dqqMinos active 1 - 1 - -

cplex_direct active 0 0 0 - -

cplexlp active 1 - - - -

qpng passive - - 1 - -

tomlab_snopt passive - - - - 0

lp_solve legacy 1 - - - -

----------------------------------------------------------------------

Total - 8 2 4 1 1

+ Legend: - = not applicable, 0 = solver not compatible or not installed, 1 = solver installed.

> You can solve LP problems using: 'glpk' - 'matlab' - 'pdco' - 'quadMinos'

> You can solve MILP problems using: 'glpk'

> You can solve QP problems using: 'pdco'

> You can solve MIQP problems using:

> You can solve NLP problems using: 'matlab'

> Checking for available updates ...

> The COBRA Toolbox is up-to-date.

>> testMgPipe

Error using prepareTest (line 353)

ibm_cplex is a required solver for the test and not available on your system.

Error in testMgPipe (line 16)

prepareTest('requiredToolboxes',requiredToolboxes, 'requiredSolvers', {'ibm_cplex'});

>> generateSystemConfigReport

> ---------------------------------- SYSTEM CONFIGURATION REPORT ----------------------------------

_____ _____ _____ _____ _____ |

/ ___| / _ \ | _ \ | _ \ / ___ \ | COnstraint-Based Reconstruction and Analysis

| | | | | | | |_| | | |_| | | |___| | | The COBRA Toolbox - 2020

| | | | | | | _ { | _ / | ___ | |

| |___ | |_| | | |_| | | | \ \ | | | | | Documentation:

\_____| \_____/ |_____/ |_| \_\ |_| |_| | http://opencobra.github.io/cobratoolbox

|

> Checking if git is installed ... Done (version: 1.8.3.).

> Checking if the repository is tracked using git ... Done.

> Checking if curl is installed ... Done.

> Checking if remote can be reached ... Done.

> Initializing and updating submodules (this may take a while)... Done.

> Adding all the files of The COBRA Toolbox ... Done.

> Define CB map output... set to svg.

> TranslateSBML is installed and working properly.

> Configuring solver environment variables ...

- [--*-] ILOG_CPLEX_PATH: /mnt/home/leejooy5/ILOG/CPLEX_Studio128/cplex/matlab/x86-64_linux

- [----] GUROBI_PATH: --> set this path manually after installing the solver ( see instructions )

- [----] TOMLAB_PATH: --> set this path manually after installing the solver ( see instructions )

- [----] MOSEK_PATH: --> set this path manually after installing the solver ( see instructions )

Done.

> Checking available solvers and solver interfaces ...Warning: File: Cplex.p Line: 965 Column: 0

Defining "changedParam" in the nested function shares it with the parent function. In a future release, to share

"changedParam" between parent and nested functions, explicitly define it in the parent function.

> In changeCobraSolver (line 435)

In initCobraToolbox (line 405)

In generateSystemConfigReport (line 72)

Done.

> Setting default solvers ... Done.

> Saving the MATLAB path ... Done.

- The MATLAB path was saved as ~/pathdef.m.

> Summary of available solvers and solver interfaces

Support LP MILP QP MIQP NLP

----------------------------------------------------------------------

gurobi active 0 0 0 0 -

ibm_cplex active 1 1 1 1 -

tomlab_cplex active 0 0 0 0 -

glpk active 1 1 - - -

mosek active 0 - 0 - -

matlab active 1 - - - 1

pdco active 1 - 1 - -

quadMinos active 1 - - - -

dqqMinos active 1 - 1 - -

cplex_direct active 0 0 0 - -

cplexlp active 1 - - - -

qpng passive - - 1 - -

tomlab_snopt passive - - - - 0

lp_solve legacy 1 - - - -

----------------------------------------------------------------------

Total - 8 2 4 1 1

+ Legend: - = not applicable, 0 = solver not compatible or not installed, 1 = solver installed.

> You can solve LP problems using: 'glpk' - 'matlab' - 'pdco' - 'quadMinos'

> You can solve MILP problems using: 'glpk'

> You can solve QP problems using: 'pdco'

> You can solve MIQP problems using:

> You can solve NLP problems using: 'matlab'

> Checking for available updates ...

> The COBRA Toolbox is up-to-date.

Elapsed time is 3.011114 seconds.

-----------------------------------------------------------------------------------------------------

MATLAB Version: 9.4.0.813654 (R2018a)

MATLAB License Number: 1110432

Operating System: Linux 3.10.0-957.5.1.el7.x86_64 #1 SMP Fri Feb 1 14:54:57 UTC 2019 x86_64

Java Version: Java 1.8.0_144-b01 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

-----------------------------------------------------------------------------------------------------

MATLAB Version 9.4 (R2018a)

Simulink Version 9.1 (R2018a)

Bioinformatics Toolbox Version 4.10 (R2018a)

Communications System Toolbox Version 6.6 (R2018a)

Computer Vision System Toolbox Version 8.1 (R2018a)

Control System Toolbox Version 10.4 (R2018a)

Curve Fitting Toolbox Version 3.5.7 (R2018a)

DSP System Toolbox Version 9.6 (R2018a)

Database Toolbox Version 8.1 (R2018a)

Econometrics Toolbox Version 5.0 (R2018a)

Embedded Coder Version 7.0 (R2018a)

Financial Toolbox Version 5.11 (R2018a)

Fixed-Point Designer Version 6.1 (R2018a)

Fuzzy Logic Toolbox Version 2.3.1 (R2018a)

Global Optimization Toolbox Version 3.4.4 (R2018a)

HDL Coder Version 3.12 (R2018a)

Image Acquisition Toolbox Version 5.4 (R2018a)

Image Processing Toolbox Version 10.2 (R2018a)

Instrument Control Toolbox Version 3.13 (R2018a)

M2HTML Toolbox - A Documentation Generator for ... Version 1.5

MATLAB Coder Version 4.0 (R2018a)

MATLAB Compiler Version 6.6 (R2018a)

MATLAB Compiler SDK Version 6.5 (R2018a)

Mapping Toolbox Version 4.6 (R2018a)

Matrix Computation Toolbox Version 1.2

Model Predictive Control Toolbox Version 6.1 (R2018a)

Neural Network Toolbox Version 11.1 (R2018a)

Optimization Toolbox Version 8.1 (R2018a)

Parallel Computing Toolbox Version 6.12 (R2018a)

Partial Differential Equation Toolbox Version 3.0 (R2018a)

RF Toolbox Version 3.4 (R2018a)

Robotics System Toolbox Version 2.0 (R2018a)

Robust Control Toolbox Version 6.4.1 (R2018a)

Signal Processing Toolbox Version 8.0 (R2018a)

SimBiology Version 5.8 (R2018a)

Simscape Version 4.4 (R2018a)

Simscape Fluids Version 2.4 (R2018a)

Simscape Multibody Version 5.2 (R2018a)

Simscape Power Systems Version 6.9 (R2018a)

Simulink 3D Animation Version 8.0 (R2018a)

Simulink Coder Version 8.14 (R2018a)

Simulink Control Design Version 5.1 (R2018a)

Simulink Design Optimization Version 3.4 (R2018a)

Stateflow Version 9.1 (R2018a)

Statistics and Machine Learning Toolbox Version 11.3 (R2018a)

Symbolic Math Toolbox Version 8.1 (R2018a)

System Identification Toolbox Version 9.8 (R2018a)

Wavelet Toolbox Version 5.0 (R2018a)

> Default shell : /bin/bash

> Version of shell : GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)

License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software; you are free to change and redistribute it.

There is NO WARRANTY, to the extent permitted by law.

> Architecture : GLNXA64

> MATLAB folder : /opt/software/MATLAB/2018a

> COBRA Toolbox root : /mnt/ufs18/home-041/leejooy5/cobratoolbox

> git version : git version 1.8.3.1

> curl version : curl 7.68.0 (x86_64-conda_cos6-linux-gnu)

> CBT_LP_SOLVER : glpk

> CBT_MILP_SOLVER : glpk

> CBT_QP_SOLVER : pdco

> CBT_MIQP_SOLVER :

> CBT_NLP_SOLVER : matlab

> GUROBI_PATH :

> ILOG_CPLEX_PATH : /mnt/home/leejooy5/ILOG/CPLEX_Studio128/cplex/matlab/x86-64_linux

> TOMLAB_PATH :

> MOSEK_PATH :

> ----------------------------------- END OF CONFIGURATION REPORT -----------------------------------

> Please send the report located in

/mnt/ufs18/home-041/leejooy5/cobratoolbox/COBRAconfigReport.log

to the developers or post it in the forum:

Ronan M.T. Fleming

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Apr 27, 2020, 7:10:23 PM4/27/20

to COBRA Toolbox

Hi Joo-Young,

there seems to be a problem with the installation of cplex. What is
the response from this call

solverName = 'ibm_cplex';
solverType = 'LP';
printLevel = 3;
validationLevel = 2;
[solverOK, solverInstalled] = changeCobraSolver(solverName,
solverType, printLevel, validationLevel)

https://github.com/opencobra/cobratoolbox/blob/develop/src/base/solvers/getSetSolver/changeCobraSolver.m

Regards,

Ronan

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----------------------------------------------------------------------------
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Leiden University.
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&
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Joo-Young Lee

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Apr 28, 2020, 10:37:19 PM4/28/20

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Hi Ronan,

Thank you for your help. The following is what I got from matlab command window.

>> solverName = 'ibm_cplex';

solverType = 'LP';

printLevel = 3;

validationLevel = 2;

[solverOK, solverInstalled] = changeCobraSolver(solverName,

solverType, printLevel, validationLevel)

[solverOK, solverInstalled] = changeCobraSolver(solverName,

↑

Error: Invalid expression. When calling a function or indexing a variable, use parentheses. Otherwise, check for

mismatched delimiters

2020년 4월 27일 월요일 오후 7시 10분 23초 UTC-4, Ronan M.T. Fleming 님의 말:

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Ronan M.T. Fleming

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Apr 28, 2020, 10:58:20 PM4/28/20

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[solverOK, solverInstalled] = changeCobraSolver(solverName,
solverType, printLevel, validationLevel); %should be all in one line

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Joo-Young Lee

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Apr 29, 2020, 4:33:24 PM4/29/20

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Hi Ronan, I re-run follwoing your suggestion.

>> solverName = 'ibm_cplex';

solverType = 'LP';

printLevel = 3;

validationLevel = 2;

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

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

> The compatibility can only be evaluated on Linux Ubuntu.

> The solver compatibility is not tested with MATLAB R2018a.

Warning: File: Cplex.p Line: 965 Column: 0

Defining "changedParam" in the nested function shares it with the parent function. In a

future release, to share "changedParam" between parent and nested functions, explicitly

define it in the parent function.

> In changeCobraSolver (line 435)

CPLEX Error 1003: Bad argument to Callable Library routine.

solverOK =

logical

0

solverInstalled =

logical

1

>>

2020년 4월 28일 화요일 오후 10시 58분 20초 UTC-4, Ronan M.T. Fleming 님의 말:

Ronan M.T. Fleming

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Apr 29, 2020, 4:58:54 PM4/29/20

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Hi,

is this a cplex rather than cobra toolbox issue:

https://www.google.com/search?q=CPLEX+Error+1003%3A+Bad+argument+to+Callable+Library+routine.&rlz=1C5CHFA_enLU788IE788&oq=CPLEX+Error++1003%3A+Bad+argument+to+Callable+Library+routine.&aqs=chrome..69i57.261j0j7&sourceid=chrome&ie=UTF-8

Regards,

Ronan

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