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I'm having trouble getting libsbml to work on Windows XP 64-bit
machine? Should it work? If so, which version should I be using?

Thanks,

Chris


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It turns out to be more complicated than using a flag ... in fact that flag
only exists on OSX. So for 64bit windows:

A) either download and install the 32bit JVM (that will work fine, and you
can use the provided libsbml libraries) or
B) generate 64bit java bindings. That is a bit harder than anticipated, but
not overly so, you will need to compile libsbml
For yourself, next generate the SWIG bindings for Java, and then slightly
alter the existing visual project file to no longer target x86 but
x64. Here the details:

Building and installing libSBML
http://sbml.org/Software/libSBML/docs/cpp-api/libsbml-installation.html

Enable a 64-Bit Visual C++ Toolset at the Command Line
http://msdn.microsoft.com/en-us/library/x4d2c09s.aspx

Configure Visual C++ Projects to Target 64-Bit Platforms
http://msdn.microsoft.com/en-us/library/9yb4317s.aspx

In the long run it might probably make sense to add a feature request that
the Java bindings are built for 64bit Java as well.

Cheers
Frank


> -----Original Message-----
> From: libsbml-development-bounces@caltech.edu [mailto:libsbml-
> development-bounces@caltech.edu] On Behalf Of Frank Bergmann
> Sent: Tuesday, June 30, 2009 5:03 PM
> To: LibSBML Development List
> Subject: Re: [libsbml-development] 64-bit libsbml
>
> Hello Chris,
>
> the released versions of libsbml (and the java bindings) only contain
> 32bit executables. If you run a 64bit Java machine, it will not be
> able to load these libraries. However i think you might be able to
> force the JVM to be instantiated in 32 bit mode by supplying the -d32
> argument.
>
> Good luck
> Frank
>
> On Jun 30, 2009, at 4:36 PM, Chris J. Myers wrote:
>
> > I'm having trouble getting libsbml to work on Windows XP 64-bit
> > machine? Should it work? If so, which version should I be using?
> >
> > Thanks,
> >
> > Chris
> >
> >
> > ____________________________________________________________
> > To manage your libsbml-development list subscription, visit
> > https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
> >
> > For a web interface to the libsbml-development mailing list, visit
> > http://sbml.org/Forums/
> >
> > For questions or feedback about the libsbml-development list,
> > contact sbml-team@caltech.edu
> >
>
> ____________________________________________________________
> To manage your libsbml-development list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>
> For a web interface to the libsbml-development mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the libsbml-development list,
> contact sbml-team@caltech.edu


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Hello Chris,

maybe a detailed stracktrace with exception error message could help
us to make sure that we are looking at the right place. The 32 bit JVM
should have worked just fine. It could be that one of the dependency
libraries, such as the XML library, bzip2 or zlib or even the MSVC
runtime libraries is missing, and that is why the wrapper library
could not be loaded.

As to how to build 64bit binaries with cygwin, i would guess just
compile the file with the -arch x86_64 or -arch x64 flag. ut honestly
i'm not the one to ask using g++ on windows :)

cheers
Frank

On Jul 6, 2009, at 4:04 PM, Chris J. Myers wrote:

> Thanks for the detailed instructions. I tried installing and using
> the 32 bit JVM on Windows XP x64, but this also failed to load the
> library file. I don't use Visual C++. Can a 64-bit library be built
> using Cygwin? Alternatively, is the SBML team planning to release a
> 64-bit version of libsbml for Windows?
>
> Cheers,
>
> Chris
>
> On Jun 30, 2009, at 6:16 PM, Frank Bergmann wrote:
>
>> It turns out to be more complicated than using a flag ... in fact
>> that flag
>> only exists on OSX. So for 64bit windows:
>>
>> A) either download and install the 32bit JVM (that will work fine,
>> and you
>> can use the provided libsbml libraries) or
>> B) generate 64bit java bindings. That is a bit harder than
>> anticipated, but
>> not overly so, you will need to compile libsbml
>> For yourself, next generate the SWIG bindings for Java, and then
>> slightly
>> alter the existing visual project file to no longer target x86 but
>> x64. Here the details:
>>
>> Building and installing libSBML
>> http://sbml.org/Software/libSBML/docs/cpp-api/libsbml-
>> installation.html
>>
>> Enable a 64-Bit Visual C++ Toolset at the Command Line
>> http://msdn.microsoft.com/en-us/library/x4d2c09s.aspx
>>
>> Configure Visual C++ Projects to Target 64-Bit Platforms
>> http://msdn.microsoft.com/en-us/library/9yb4317s.aspx
>>
>> In the long run it might probably make sense to add a feature
>> request that
>> the Java bindings are built for 64bit Java as well.
>>
>> Cheers
>> Frank
>>
>>
>>> -----Original Message-----
>>> From: libsbml-development-bounces@caltech.edu [mailto:libsbml-
>>> development-bounces@caltech.edu] On Behalf Of Frank Bergmann
>>> Sent: Tuesday, June 30, 2009 5:03 PM
>>> To: LibSBML Development List
>>> Subject: Re: [libsbml-development] 64-bit libsbml
>>>
>>> Hello Chris,
>>>
>>> the released versions of libsbml (and the java bindings) only
>>> contain
>>> 32bit executables. If you run a 64bit Java machine, it will not be
>>> able to load these libraries. However i think you might be able to
>>> force the JVM to be instantiated in 32 bit mode by supplying the -
>>> d32
>>> argument.
>>>
>>> Good luck
>>> Frank
>>>
>>> On Jun 30, 2009, at 4:36 PM, Chris J. Myers wrote:
>>>
>>>> I'm having trouble getting libsbml to work on Windows XP 64-bit
>>>> machine? Should it work? If so, which version should I be using?
>>>>
>>>> Thanks,
>>>>
>>>> Chris
>>>>
>>>>
>>>> ____________________________________________________________
>>>> To manage your libsbml-development list subscription, visit
>>>> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>>>>
>>>> For a web interface to the libsbml-development mailing list, visit
>>>> http://sbml.org/Forums/
>>>>
>>>> For questions or feedback about the libsbml-development list,
>>>> contact sbml-team@caltech.edu
>>>>
>>>
>>> ____________________________________________________________
>>> To manage your libsbml-development list subscription, visit
>>> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>>>
>>> For a web interface to the libsbml-development mailing list, visit
>>> http://sbml.org/Forums/
>>>
>>> For questions or feedback about the libsbml-development list,
>>> contact sbml-team@caltech.edu
>>
>>
>> ____________________________________________________________
>> To manage your libsbml-development list subscription, visit
>> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>>
>> For a web interface to the libsbml-development mailing list, visit
>> http://sbml.org/Forums/
>>
>> For questions or feedback about the libsbml-development list,
>> contact sbml-team@caltech.edu
>
> ____________________________________________________________
> To manage your libsbml-development list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>
> For a web interface to the libsbml-development mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the libsbml-development list,
> contact sbml-team@caltech.edu
>

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Hello Chris,

Hmm ... the console output still has not enough information for me to act
on, the java -version output is next to useless for me. However if you would
start java as:

"\Program Files (x86)\Java\jdk1.6.0_14\bin\java.exe"

We would be sure that it is indeed the 32 bit version running.

The next question to ask then is which libsbml installer you were using. For
example if you have been downloading this one:

http://sourceforge.net/projects/sbml/files/libsbml/libSBML-3.4.0-win-libxml2
-vc90.exe

you would need the visual C runtime:

http://www.microsoft.com/downloads/details.aspx?FamilyID=a5c84275-3b97-4ab7-
a40d-3802b2af5fc2

(don't mind the x86 bit)

Good luck ...

Best
Frank

> -----Original Message-----
> From: libsbml-development-bounces@caltech.edu [mailto:libsbml-
> development-bounces@caltech.edu] On Behalf Of Chris J. Myers
> Sent: Tuesday, July 07, 2009 8:28 AM
> To: LibSBML Development List
> Subject: Re: [libsbml-development] 64-bit libsbml
>
> Hi Frank,
>
> Below is the code and attached is the error message with stack trace:
>
> String varname;
> if (System.getProperty("mrj.version") != null)
> varname = "DYLD_LIBRARY_PATH"; // We're on a
> Mac.
> else
> varname = "LD_LIBRARY_PATH"; // We're not on
a
> Mac.
> try {
> System.loadLibrary("sbmlj");
> // For extra safety, check that the jar file
is
> in the
> // classpath.
> Class.forName("org.sbml.libsbml.libsbml");
> }
> catch (UnsatisfiedLinkError e) {
> StringWriter sw = new StringWriter();
> PrintWriter pw = new PrintWriter(sw);
> e.printStackTrace(pw);
> System.out.println("Error = " + sw.toString());
>
> System.err.println("Error: could not link
with
> the libSBML library."
> + " It is likely\nyour " +
varname
> + " environment variable
does not
> include\nthe"
> + " directory containing the
> libsbml library file.");
> System.exit(1);
> }
>
> I'm not sure if this is an issue, but I'm running Windows XP x64 using
> Parallels on a Mac. I've also tried running Windows 2000 which is 32-
> bit OS using Parallels, and this works fine. Also, if I comment out
> the loadLibrary, the parts that do not depend on libsbml work fine.
>
> Cheers,
>
> Chris


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> This did the trick. It now works.
>

I'm glad you managed to sort this out - Thanks Frank for your input.

We (libsbml-team) are currently considering whether we need to do 64 bit
builds for windows. Since building all the files for each installer
variant is time consuming we are wondering which libraries people would
be particularly interested in ...

Thanks

Sarah
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>
> We (libsbml-team) are currently considering whether we need to do 64
> bit
> builds for windows. Since building all the files for each installer
> variant is time consuming we are wondering which libraries people would
> be particularly interested in ...
>

We use either the libxml or the expat bindings. Going forward I think expat
will sooner or later stop working for us, as there is no Xpath support in
there. So if we have only one 64 bit build I prefer it to be libxml based.
However, the resulting library is hopefully not called libsbml.dll, as this
might break things later on. Oh and one more thing on the wish list, could
you please link it against static versions of xml parser, and the zip + bzip
libraries? And perhaps using the /MT switch to link against the static
runtime? I think that would then limit all compatibility problems like we
have seen them in the past to an absolute minimum


Cheers
Frank

> Thanks
>
> Sarah
> ____________________________________________________________
> To manage your libsbml-development list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/libsbml-development
>
> For a web interface to the libsbml-development mailing list, visit
> http://sbml.org/Forums/
>
> For questions or feedback about the libsbml-development list,
> contact sbml-team@caltech.edu


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