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* Akiya Jouraku <jouraku@bio.keio.ac.jp> [2010-02-11 08:25] writes:
> Hello Lucian,
>
> Regarding your problem, I have the following questions:
>
> (1) Could you let us know the following information?
>
> 1) version of Ubuntu
> 2) architecture (i386 or x86_64)
> 3) vendor/version of Java (e.g. Sun/1.6.0_07, OpenJDK/1.6.0_0)

Ubuntu 9.04, i386, and Sun 1.6.0_16-b01

> (2) Could you send us a clash log generated by JVM ?

I don't have any clash log, just a segmentation fault, sadly. I tried
strace, but I think it was running stuff in parallel, so the bit where it
crashed is hidden somewhere in that huge output.

> (3) Does the odesolver work fine on your environment?

Yes, they both work fine separately. And my sample code works fine if I
reverse the order of loading the libraries (load libsbml first, then the
odesolver). And for the heck of it, I tried also loading a different
library that was *not* compiled for java just to see what happened, and if
I load odesolver -> random thing -> sbmlj, it crashes when it tries to
load sbmlj, but if I load random thing -> odesolver -> sbmlj, it runs
fine.

(this is true for two completely different shared libraries that were
hanging out in /usr/local/lib--cellml, which I had compiled myself, and
vtkCommon, which was part of some package I downloaded.)

It is so weird!

> (4) Is JSim compiled on the same host?

Yes. It is possible that there could be some flag used for a library here
that is somehow incompatible with a flag used to compile the JSim
libraries. JSim was developed on RedHat, and I had to extensively modify
the Makefile system to get it to compile on Ubuntu without really knowing
what I was doing, but I don't really know where to start.

Since the first email, I've tried my sample program on Windows using the
pre-compiled libraries for both JSim and libSBML, and encountered no
problems. I'm about to go try it on a RedHat system to see if the error
follows me there...

Thanks for following up!

-Lucian

>
>
> Thanks,
>
> Akiya
>
> Lucian Smith <lpsmith@spod-central.org> wrote
> > So, I'm working on a smallish project to use libsbml under java for use
> > with a different project, written in java (JSim). However, the libsbml
> > library and the other project's library seem to be clashing, and I'm not
> > sure where to look to start debugging the problem.
> >
> > (I'm using ubuntu and a version of libsbmlj that I compiled myself from
> > the 4.0.1 source distribution)
> >
> >
> > Here's a small java class that demonstrates the problem:
> >
> >
> > import org.sbml.libsbml.*;
> >
> > public class test {
> > public static void main(String[] args) {
> > System.out.println("Hello world.");
> > System.loadLibrary("odesolver");
> > System.out.println("Loaded odesolver");
> > System.loadLibrary("sbmlj");
> > System.out.println("Loaded sbmlj.");
> > SBMLReader reader = new SBMLReader();
> > System.out.println("Ran something using libsbml");
> > }
> > }
> >
> > Compiling this with javac works fine if I set the classpath to point at
> > the libsbmlj.jar file and the various .jar files that the 'odesolver'
> > uses.
> >
> > Then running it under java, I use the same classpath, and point
> > java.library.path to the directory with libsbml*.so and the directory with
> > the odesolver's .so files.
> >
> > I get the following:
> >
> > Hello world.
> > Loaded odesolver
> > Segmentation fault
> >
> >
> > If I reverse the order in which I load the libraries, suddenly everything
> > works!
> >
> > Hello world.
> > Loaded sbmlj.
> > Loaded odesolver
> > Ran something using libsbml
> >
> > (I did run nm on the various .so files, but didn't find any conflicts in
> > the text symbols, at least.)
> >
> > Anyone have some insight as to what's going wrong? Thanks!
> >
> > -Lucian
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>
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