Re: [SOSlib-discuss] [SOSlib-devel] [ sbmlsolver-Bugs-1924288 ] Only one timepoint

[Rainer M. <ra...@tb...>]

Hi Gabriel,

The 1.6.0 version requires SUNDIALS 2.1.1. This is mentioned here:

http://www.tbi.univie.ac.at/~raim/odeSolver/doc/installGnu.html

but unfortunately not in the README/INSTALL instructions of the 
distribution (as back then, 2.1.1 was the latest version). Sorry for that.

Please could you try to remove the new version of SUNDIALS from your 
include and lib directories (maybe they have a make uninstall ?), 
install the 2.1.1 version, and then try again to compile SOSlib 1.6.0?

Alternatively, you could go for the CVS version of SOSlib which should 
run quite stable and compile easier then 1.6.0.

However, this requires the SUNDIALS 2.3.0 which you already have BUT 
also libSBML 3.2.0 (latest). In this case, please make sure to 
completely remove the old libSBML headers before installing SOSlib!!!

The CVS version has a couple of nice new features and should also run 
much faster for large models, if you use the compile option (-c for 
command-line, CvodeSettings_setCompileFunctions(settings, 1) for library 
use).

Unfortunately, we don't know yet when the next official release will 
happen :( but there should be few changes left with respect to current CVS.

Please let us know (either email me personally or the sbmlsolver-discuss 
list, see CC address) if you run into further problems!!

best regards,
Rainer









SourceForge.net wrote:
> Bugs item #1924288, was opened at 2008-03-24 13:23
> Message generated for change (Tracker Item Submitted) made by Item Submitter
> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1924288&group_id=139893
> 
> Please note that this message will contain a full copy of the comment thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: solver malfunction
> Group: None
> Status: Open
> Resolution: None
> Priority: 5
> Private: No
> Submitted By: Gabriel Plantat (gabrieljps)
> Assigned to: Nobody/Anonymous (nobody)
> Summary: Only one timepoint
> 
> Initial Comment:
> Hello,
> I have in fact two problems, and i think that i need the solution to only one of them :)
> I'm trying to install the verison 1.6.0 on a Kubuntu (Linux) operating system. I have installed the libsbml.2.3.4 (compiled with the expat library) and sundials.2.3.0 libraries in a local directory, and when i compile the SBML_odeSolver, it crashes. I have set the --with-libsbml option to the directory where the libraries are, and it produces the error:
> 
> checking for SBML Library Version... expr: syntax error
> expr: syntax error
> expr: syntax error
> ./configure: line 4175: test: -eq: unary operator expected
> configure: found SBML Library Version
> checking correct functioning of SBML... yes
> ./configure: line 4278: test: -eq: unary operator expected
> checking correct functioning of SUNDIALS CVODE... no:
>                    CFLAGS=-g -O2 -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0//include
>                    LDFLAGS= -L/home/gabrieljps/trabajos/synthbio2/genetdes_3.0//lib
>                    LIBS= -lsundials_kinsol -lsundials_cvodes -lsundials_cvode -lsundials_nvecserial -lsundials_shared -lm
> configure: error: Can not link to SUNDIALS CVODE Library
> 
> 
> 
> If i change the directory to where the files .so are (the same directory with a /lib appended), it gives this error:
> 
> checking for SBML Library Version... configure: found SBML Library Version 2.3.4
> checking correct functioning of SBML... no:
>                    CFLAGS=-g -O2 -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/include -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/include/sbml
>                    LDFLAGS= -Wl,-rpath,/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/lib -L/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/lib
>                    LIBS= -lxerces-c -lsbml
> configure: error: Can not link to SBML Library:
>                   Please, make sure to use libSBML version >= 2.3.2
> 
> 
> So i began using the 1.6pre version, which compiles. But doesn't seem to be working properly. I have tried the integrate exemple file with the MAPK.xml file, and when i expect all the results from the integration, it just gives me one time. I have printed the results->timepoints variable and it is set to 1.
> Even further, in this file the third parameter to be given is supposed to be the number of time steps, but if the number of steps is greater than the ending time, it crashes. On the contrary, if it is not, it doesn't, even if the number of steps is lower than 1 (0.1 for exemple)! 
> Anyway, i have used the MAPK.xml file given as an exemple with the library, and i get only the initial conditions, and no other point of the integration.
> 
> I think that if i can integrate the function or intall the 1.6.0 version, i will have the problem solved. Thank you for your help!
> 
> Gabriel PLANTAT.
> Ecole Polytechnique's student.
> gab...@gm...
> 
> 
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