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Hello Neil,

bad news, I also get your crash with your binaries:

Invalid memory access of location 00000000 rip=83da8ae1

Segmentation fault

the debugger claims it to be a bad access here:

1 libsbml.dylib 0x000000011306320b
LibXMLParser::~LibXMLParser() + 107
2 libsbml.dylib 0x000000011306c074
XMLInputStream::~XMLInputStream() + 134
3 libsbml.dylib 0x000000011306c121
XMLInputStream::~XMLInputStream() + 21
4 libsbml.dylib 0x0000000113031d3e
SBMLReader::readInternal(char const*, bool) + 842
5 libsbml.dylib 0x00000001130327d6
SBMLReader::readSBML(std::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&) + 42
6 libsbmlj.jnilib 0x0000000112f63370
Java_org_sbml_libsbml_libsbmlJNI_SBMLReader_1readSBML + 212

which of course makes no sense whatsoever as the free in
~LibXMLParser() is guarded. So at this point the question to ask is,
whether the 64bit binaries of libsbml work as expected. So you might
want to try to build the echoSBML c/c++ example (for 64bit) and try
that. this would isolate the problem.

Maybe this is the point to ask Akiya to step in. As he might be more
familiar with the issue.

best
Frank

On Feb 20, 2009, at 9:09 AM, Neil Swainston wrote:

> Hi Frank,
>
> Thanks for the suggestions. I'll look into those.
>
> In the mean time, however, I've zipped up the libraries and left them
> here..,
>
> ftp://ftp.dbkgroup.org/pub/libsbml.zip
>
> If you or anyone else has five minutes to look over them, then that
> would be great.
>
> Best wishes,
>
> Neil.
>
> On 19 Feb 2009, at 17:12, Frank Bergmann wrote:
>
>> hello neil,
>>
>> thank you for the detailed answer. unfortunately we don't really know
>> what went wrong at all, was there any output in console.app, that
>> related to it? Have you tried running with the -d64 bit flag, to
>> ensure you are in 64bit data mode (and yes i know that java6 is only
>> for 64bit, but it doesn't hurt trying). What you might want to do, is
>> to ensure that the library contains debug symbols and then try and
>> attach gdb to at least glean where things go wrong.
>>
>> or you could zip up all your libraries (ad jar files) and put them
>> somewhere for us to check.
>>
>> best
>> Frank
>>
>>
>> On Feb 19, 2009, at 1:42 AM, Neil Swainston wrote:
>>
>>> Hi Frank,
>>>
>>> Thanks for your response.
>>>
>>> I'll try to fill in some gaps...
>>>
>>> My build procedure was as follows:
>>>
>>> Ensure that java -version and javac -version displayed version 1.6.
>>>
>>> export CXXFLAGS="-arch x86_64"
>>> export CFLAGS="-arch x86_64"
>>> export LDFLAGS="-arch x86_64"
>>> ./configure --with-java
>>> make
>>> make install
>>>
>>> All ran without errors. If its of any interest, the output after
>>> running ./configure was as follows:
>>>
>>> ----------------------------------------------------------------------
>>> libSBML version 3.3.1
>>> ----------------------------------------------------------------------
>>>
>>> More information and the latest version are available online at
>>> http://sbml.org/Software/libSBML
>>>
>>> Please report problems using the issue tracker at
>>> http://sbml.org/software/libsbml/issue-tracker
>>>
>>> To contact the developers directly, email libsbml-team@caltech.edu
>>>
>>> Configured on host "swainston3.mib.man.ac.uk"
>>> host type = darwin
>>> host vendor = apple
>>> host operating system = darwin9.6.0
>>> host CPU architecture = i386
>>>
>>> General build flags:
>>> CC = gcc
>>> CXX = g++
>>> CFLAGS = -arch x86_64
>>> CXXFLAGS = -arch x86_64
>>> CPPFLAGS = -DMACOSX
>>> LDFLAGS = -arch x86_64
>>> LIBS = -lm -lz -lbz2
>>>
>>> XML parser library configuration:
>>> XML library = libxml2
>>> CPPFLAGS for XML = -I/usr/include/libxml2
>>> LDFLAGS for XML =
>>> LIBS for XML = -L/usr/lib -lxml2 -lz -lpthread -
>>> licucore -lm
>>>
>>> Other libSBML configuration settings:
>>> Installation $prefix = /usr/local
>>> Using Java with path = /usr/bin/java
>>> Using zlib with path = autodetect
>>> Using bzip2 with path = autodetect
>>>
>>> Other potentially important settings:
>>> Compression support enabled for .zip, .gz and .bz2 files
>>> Value of $DYLD_LIBRARY_PATH =
>>> Value of $CLASSPATH for Java =
>>> ----------------------------------------------------------------------
>>>
>>> This generated the required files in /usr/local/lib.
>>>
>>> Attempting to compile and run one of the small test programs with
>>> these files returned the following error:
>>>
>>> swainston3:java neilswainston$ pwd
>>> /Developer/Applications/libsbml-3.3.1/examples/java
>>> swainston3:java neilswainston$ javac -cp /usr/local/lib/libsbmlj.jar
>>> readSBML.java
>>> swainston3:java neilswainston$ java -cp .:/usr/local/lib/
>>> libsbmlj.jar -
>>> Djava.library.path=/usr/local/lib/ readSBML /Users/neilswainston/
>>> Desktop/sbml.xml
>>> Invalid memory access of location 00000000 rip=82fa4ae1
>>>
>>> Segmentation fault
>>>
>>> Looking at the libraries more closely...
>>>
>>> file returns the following:
>>>
>>> swainston3:~ neilswainston$ file /usr/local/lib/libsbml.dylib
>>> /usr/local/lib/libsbml.dylib: Mach-O 64-bit dynamically linked
>>> shared
>>> library x86_64
>>>
>>> swainston3:~ neilswainston$ file /usr/local/lib/libsbmlj.jnilib
>>> /usr/local/lib/libsbmlj.jnilib: Mach-O 64-bit bundle x86_64
>>>
>>> otool returns the following:
>>>
>>> swainston3:~ neilswainston$ otool -L /usr/local/lib/libsbmlj.jnilib
>>> /usr/local/lib/libsbmlj.jnilib:
>>> ../libsbml.dylib (compatibility version 0.0.0, current version
>>> 3.3.1)
>>> /usr/lib/libxml2.2.dylib (compatibility version 9.0.0, current
>>> version 9.16.0)
>>> /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
>>> 1.2.3)
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>>> version 111.1.3)
>>> /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current
>>> version 36.0.0)
>>> /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current
>>> version 1.0.4)
>>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
>>> version 7.4.0)
>>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
>>> version 1.0.0)
>>>
>>> swainston3:~ neilswainston$ otool -L /usr/local/lib/libsbmlj.jnilib
>>> /usr/local/lib/libsbmlj.jnilib:
>>> ../libsbml.dylib (compatibility version 0.0.0, current version
>>> 3.3.1)
>>> /usr/lib/libxml2.2.dylib (compatibility version 9.0.0, current
>>> version 9.16.0)
>>> /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
>>> 1.2.3)
>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>>> version 111.1.3)
>>> /usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current
>>> version 36.0.0)
>>> /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current
>>> version 1.0.4)
>>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
>>> version 7.4.0)
>>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
>>> version 1.0.0)
>>>
>>>
>>> So, I'm a little stuck... Sadly I cannot really continue with Java 5
>>> as I'm needing all manner of webservice goodies that come shipped
>>> with
>>> Java 6.
>>>
>>> Any help, as ever, would be appreciated.
>>>
>>> Cheers,
>>>
>>> Neil.
>>>
>>>
>>> On 18 Feb 2009, at 17:48, Frank Bergmann wrote:
>>>
>>>> Hello Neil,
>>>>
>>>> IMHO its still to early for Java6 on OSX, there are still too many
>>>> 32bit machines around. Still to your problem at hand, could you
>>>> please
>>>> verify that the libsbml binaries you have list the following
>>>> architectures:
>>>>
>>>> if you run: file <libsbmlj.jnilib/dylib/libsbml.dylib>
>>>>
>>>> you want to have listed there: i386, ppc AND x86_64 (maybe even
>>>> ppc64,
>>>> as there was that one developer preview of Java6 for ppc64), and
>>>> that
>>>> is for all dependency librarys, (Just for good measure, otool -L
>>>> shows
>>>> all dependency libraries).
>>>>
>>>> Oh and then of course you want to make sure that the correct
>>>> library
>>>> is being picked up, by making sure that the java.library.path is
>>>> set
>>>> up correctly ...
>>>>
>>>> thats all we can say without more information
>>>>
>>>> cheers
>>>> Frank
>>>>
>>>>
>>>>
>>>> On Feb 18, 2009, at 2:19 AM, Neil Swainston wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> Sorry to go over old ground here, but I still didn't manage to get
>>>>> libsbml working with 64-bit Java v6 on a Mac. (There's an old
>>>>> thread
>>>>> also named 'Using libsbml from Java on MacOSX' on the forum).
>>>>>
>>>>> I'm sure that someone out there in cyberland is happily using
>>>>> Macs,
>>>>> libsbml and 64-bit Java 6 in perfect tandem? If so, I envy you
>>>>> greatly
>>>>> and seek your advice.
>>>>>
>>>>> I'm assuming that by default, libsbml is built as 32-bit, so when
>>>>> 64-
>>>>> bit Java attempts to call the libraries via JNI, problems arise.
>>>>>
>>>>> I've attempted to build libsbml with -x64 flags (as suggested by
>>>>> Frank
>>>>> - many thanks) but this doesn't seem to work.
>>>>>
>>>>> Any advice would be hugely appreciated.
>>>>>
>>>>> Cheers.
>>>>>
>>>>> Neil.
>>>>>
>>>>> Neil Swainston
>>>>> Experimental Officer
>>>>>
>>>>> Manchester Centre for Integrative Systems Biology
>>>>> Manchester Interdisciplinary Biocentre
>>>>> University of Manchester
>>>>> Manchester M1 7DN
>>>>> England
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ____________________________________________________________
>>>>> 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
>>>
>>>
>>> Neil Swainston
>>> Experimental Officer
>>>
>>> Manchester Centre for Integrative Systems Biology
>>> Manchester Interdisciplinary Biocentre
>>> University of Manchester
>>> Manchester M1 7DN
>>> England
>>>
>>>
>>>
>>>
>>>
>>> ____________________________________________________________
>>> 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
>
>
> Neil Swainston
> Experimental Officer
>
> Manchester Centre for Integrative Systems Biology
> Manchester Interdisciplinary Biocentre
> University of Manchester
> Manchester M1 7DN
> England
>
>
>
>
>
> ____________________________________________________________
> 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

____________________________________________________________
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http://sbml.org/Forums/

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