Forums

Hello Nicole,

sorry that you are having a hard time with this. Lets go through it step by step. Could you please first provide me with the following information :

- which libsbml version are you trying to install
- which SBML Toolbox are you trying to install
- what Matlab version do you have installed
- on what Linux distribution are you running.

I think you need to start over as something on your system is strange (there should be no src/sbml directory below the bindings/matlab directory). All you should need to do, in order to use LIBSBML with the matlab bindings on linux x64 is the following:

- download the latest libsbml for example:
http://sourceforge.net/projects/sbml/files/libsbml/5.4.1/stable/libsbml-5.4.1-src.tar.gz/download

- unpack :

tar zxf libsbml-5.4.1-src.tar.gz

- configure:

cd libsbml-5.4.1
./configure --with-matlab=<full path to the matlab root directory where there exists a file ./bin/matlab > -- prefix=<some directory where you have write access to>

- compile

make

- install

make install


If any of the above steps fail, please mail me:

- the precise error message you have (for example the console output)
- the file config.log in the libdsbml directory

Cheers
Frank

On Apr 24, 2012, at 7:52 PM, Nicole wrote:

>
> Hi! I am a graduate student in the process of trying to open a model from the BioModels Database using SBToolbox 2 (with SPBD). SBToolbox2 requires SBML toolbox and libsbml to be installed.
>
> I have installed all 4 programs onto both Windows and Mac platforms. However when using commands like SBedit and SBmodel in SBtoolbox 2, the commands took several hours to complete in MATLAB. So the decision was made to try to get all the toolboxes installed onto the linux supercomputer that we have access to.
>
> I have been trying to follow the instructions for installation of libsbml and SBMLtoolbox for linux. I did ./configure originally not realizing that I had to do ./configure --with-matlab. Originally ./configure followed by make and make install had no errors but matlab wasn't finding the bindings when doing "isbindinginstalled.m." I then uninstalled the bindings and did ./configure --with-matlab a new error appeared. The error was:
> ----
> /home/cnicole1/ithorpe_common/cnicole1/MATLAB/libsbml/bindings/matlab/config/.././doltlibtool --mode=compile --tag=CXX g++ -I. -I/umbc/research/ithorpe/common/cnicole1/MATLAB/libsbml/bindings/matlab/src -DLINUX -DPACKAGE_VERSION=\"m4_esyscmd_s(cat VERSION.txt)\" -I/usr/include/libxml2 -DUSE_LIBXML -DUSE_ZLIB -DUSE_BZ2 -MT AlgebraicRule.lo -MD -MP -MF ".deps/AlgebraicRule.Po" -c -o AlgebraicRule.lo AlgebraicRule.cpp
> /bin/sh: -c: line 0: syntax error near unexpected token `('
> /bin/sh: -c: line 0: `/home/cnicole1/ithorpe_common/cnicole1/MATLAB/libsbml/bindings/matlab/config/.././doltlibtool --mode=compile --tag=CXX g++ -I. -I/umbc/research/ithorpe/common/cnicole1/MATLAB/libsbml/bindings/matlab/src -DLINUX -DPACKAGE_VERSION=\"m4_esyscmd_s(cat VERSION.txt)\" -I/usr/include/libxml2 -DUSE_LIBXML -DUSE_ZLIB -DUSE_BZ2 -MT AlgebraicRule.lo -MD -MP -MF ".deps/AlgebraicRule.Po" -c -o AlgebraicRule.lo AlgebraicRule.cpp'
> make[3]: *** [AlgebraicRule.lo] Error 2
> make[3]: Leaving directory `/umbc/research/ithorpe/common/cnicole1/MATLAB/libsbml/bindings/matlab/src/sbml'
> make[2]: *** [all-this-dir] Error 2
> make[2]: Leaving directory `/umbc/research/ithorpe/common/cnicole1/MATLAB/libsbml/bindings/matlab/src/sbml'
> make[1]: *** [sbml-recurse] Error 2
> make[1]: Leaving directory `/umbc/research/ithorpe/common/cnicole1/MATLAB/libsbml/bindings/matlab/src'
> make: *** [src-recurse] Error 2
> make: Leaving directory `/umbc/research/ithorpe/common/cnicole1/MATLAB/libsbml/bindings/matlab'
> ----
> My advisor and I tried looking into the algebraic rule file but could not figure out why it wasn't working. Does anyone have helpful hints on how to install libsbml onto linux where I am not an admin? Do I need an admin to install these for me?
>
> Also when trying to use install.m to install SBMLtoolbox I get the following error:
> -----
> 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
>
> libSBML MATLAB binding not found
>
> NOTE: This is not a fatal error.
> You will not be able to import or export SBML but can still use the toolbox
> to create and manipulate MATLAB_SBML structures
>
> Installation failed
> The directories were not added to the Path
>
> -----
> I am not sure why the "Installation failed, the directories were not added to the path" is not working because when I type the exact commands the script is doing at that point, MATLAB adds the path. I can not figure out why its not finding the binding until I have installed the binding correctly.
>
> Do I need to be an administrator to do all these installs? If so I will need to have the exact instructions of how to install to give to the supercomputer support staff.
>
> Thanks for any help you can provide. I really just want to start with my research but I cannot do so until all 4 toolboxes are installed on the linux machine.
>
> --
> Nicole C.
> UMBC graduate student
> Computational Chemistry
> ____________________________________________________________
> To manage your sbml-interoperability list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability
>
> For a web interface to the sbml-interoperability mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the sbml-interoperability list,
> contact sbml-team@caltech.edu

____________________________________________________________
To manage your sbml-interoperability list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability

For a web interface to the sbml-interoperability mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the sbml-interoperability list,
contact sbml-team@caltech.edu