Re: Using libsbml from Java on MacOSX
23 Feb '09 04:10
Hello Frank and Neil,
Thanks for your detailed information.
Frank Bergmann <email@example.com> wrote
> 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.
I just tried Neil's binaries on MacOSX 10.5.6/Intel Core2 Duo.
Unfortunately, I also got the Invalid memory access error when
running example Java programs (built by Java 1.6) with Neil's binaries.
Also, I built the Java bindings with -arch x86_64 flag on my MacOSX and
got the same error.
(I tried SWIG 1.3.36, 1.3.37, and 1.3.38, "-O0" (no optimization) g++ option,
but got the same result.)
Since C++ example works fine with the x86-64 C++ library (Neil's libsbml.dylib)
and Java bindings of x86-64 binaries (built by x86-64 g++ and x86-64 java 1.6)
on Linux/x86_64 (e.g. Cent5.2, Ubuntu8.10) works fine, there might be x86-64
JNI specific problem on MacOSX but currently I have no clue about this...
I'll continue to track this problem.
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