Chronological Thread 

< Chronological >      < Thread >

---

On 11/08/11 09:25, Lucian Smith wrote:
> I am getting an odd segfault in Telicems when I have compiled CellML on
> red hat linux to have a 32-bit runtime (-m32). I don't have the problem
> at all on ubuntu.

Hi Lucian,

It is hard to work out what is going on there from the information you
have given.

A few possible things to try:
* This type of issue can occasionally happen if some headers change
between parts of the code being compiled, and so expect different
structures - it is possible you compiled, updated your C++ headers (or
mixed platforms somehow) and then did a partial compile; have you tried
a completely clean build to see if the problem still happens?
* Are you sure your libstdc++ matches the headers you compiled with?
I note you mention using -m32, so I'm assuming you needed to do this
because you are building on a 64 bit system? However, you are loading
/usr/lib/libstdc++.so.6, which is usually the location for the 64-bit
libstdc++ on 64 bit systems - are you running this in a separate system
/ container, possibly with a different version of libstdc++?
* There is the possibility of a compiler bug, especially if you are
using an old gcc; does this happen at different optimisation levels
(e.g. try going from -O2 to -O0 and see if it is still a problem)?

If you still don't get it working, a bit more information would help
track this issue down:

* What distribution version exactly are you using? Can we have an
account on the system to debug the problem?
* What program are you using to call into the CellML API, and if it
is complex, can you reproduce this problem with a very simple program?
* What gcc / libstdc++ version are you using for this test?

If you still can't get this working, I'd also suggest filing a tracker
item at https://tracker.physiomeproject.org so this doesn't get forgotten.

Best wishes,
Andrew

>
> Here's the gdb stack trace from the segfault:
>
> (gdb) bt
> #0 0x00c04919 in __gnu_cxx::__exchange_and_add(int volatile*, int) ()
> from /usr/lib/libstdc++.so.6
> #1 0x00be7f9e in std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >::_M_mutate(unsigned int, unsigned int, unsigned
> int) ()
> from /usr/lib/libstdc++.so.6
> #2 0x00be800a in std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >::_M_replace_safe(unsigned int, unsigned int, char
> const*, unsigned int) () from /usr/lib/libstdc++.so.6
> #3 0x00be80a5 in std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >::assign(char const*, unsigned int) () from
> /usr/lib/libstdc++.so.6
> #4 0x00be8225 in std::basic_string<char, std::char_traits<char>,
> std::allocator<char> >::operator=(char const*) () from
> /usr/lib/libstdc++.so.6
> #5 0xf78b4e32 in TeLICeMSLValue::release_storage (this=0xf78d3a88)
> at /user3/lpsmith/cellml-api/TeLICeMS/sources/TeLICeMStateScan.hxx:94
> #6 0xf78b4fc9 in TeLICeMSLValue::string (this=0xf78d3a88, aStr="g_init")
> at /user3/lpsmith/cellml-api/TeLICeMS/sources/TeLICeMStateScan.hxx:168
> #7 0xf78b427e in TeLICeMStateScan::yylex (this=0xffffceb8)
> at TeLICeMS/sources/TeLICeMScan.l:286
> #8 0xf789d226 in telicem_lex (aLValue=0xffffc99c, aLexer=0xffffceb8)
> at /user3/lpsmith/cellml-api/TeLICeMS/sources/TeLICeMSImpl.cpp:1268
> #9 0xf78bb9d9 in telicem_parse (aLexer=0xffffceb8,
> aParseTarget=0xffffcf40)
> at /user3/lpsmith/cellml-api/TeLICeMParse.gen.cpp:2361
> #10 0xf78aa002 in CDA_TeLICeMService::parseMaths (this=0x805edc8,
> aDoc=0x8060c3c, aMathText=0x8059acc L"g_init = 3 * x")
> at /user3/lpsmith/cellml-api/TeLICeMS/sources/TeLICeMSImpl.cpp:102
> #11 0xf7f78971 in Module::AddCellMLMathTo (this=0x8055260, formula=
> Traceback (most recent call last):
> File "/usr/share/gdb/python/libstdcxx/v6/printers.py", line 469, in
> to_string
> return self.val['_M_dataplus']['_M_p'].string (encoding, length = len)
> Runtime
>
> The 'AddCellMLMathTo' function is mine; the source code is:
>
> RETURN_INTO_OBJREF(ts, iface::cellml_services::TeLICeMService,
> CreateTeLICeMService());
> std::wstring wform(makeUTF16(formula));
> RETURN_INTO_OBJREF(tmr, iface::cellml_services::TeLICeMMathResult,
> ts->parseMaths(doc, wform.c_str()));
> // XXX it would be good to check tmr->errorMessage() and log the error -
> Andrew Miller
> RETURN_INTO_OBJREF(math, iface::mathml_dom::MathMLElement,
> tmr->mathResult());
>
> (the offending line is the 'RETURN_INTO_OBJREF(tmr,[...]);' bit.)
>
> Running it through valgrind gives an error at the exact same moment, but
> perhaps it's helpful:
>
> ==25453==
> ==25453== Process terminating with default action of signal 11 (SIGSEGV)
> ==25453== Bad permissions for mapped region at address 0x662D43D
> ==25453== at 0xC04919: __gnu_cxx::__exchange_and_add(int volatile*,
> int) (in /usr/lib/libstdc++.so.6.0.8)
>
> (and then the same back trace as gdb)
>
> The problem seems to be, weirdly enough:
>
> (gdb) frame 5
> #5 0xf78b4e32 in TeLICeMSLValue::release_storage (this=0xf78d3a88)
> at /user3/lpsmith/cellml-api/TeLICeMS/sources/TeLICeMStateScan.hxx:94
> 94 mString = "";
>
> So there has to be something weird with memory management going on.
>
> It doesn't seem to matter what string I'm asking Telicems to parse; they
> all crash at the same point.
>
> -Lucian
> _______________________________________________
> cellml-tools-developers mailing list
> cellml-tools-developers at cellml.org
> http://lists.cellml.org/mailman/listinfo/cellml-tools-developers

---

• [cellml-dev] segfault in Telicems, Lucian Smith, 08/11/2011
  • [cellml-dev] segfault in Telicems, Andrew Miller, 08/17/2011
    • [cellml-dev] segfault in Telicems, Lucian Smith, 08/24/2011

---

Archive powered by MHonArc 2.6.18.