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[cellml-dev] compiling Telicims


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  • From: ak.miller at auckland.ac.nz (Andrew Miller)
  • Subject: [cellml-dev] compiling Telicims
  • Date: Wed, 29 Dec 2010 12:54:48 +1300
On 29/12/10 12:28, Lucian Smith wrote:
> OK, inching along here...
>
> One positive update is that I discovered in the latest Windows build
> without xulrunner that I can actually click on the test .exe programs
> produced by the cellml API and they run instead of saying something along
> the lines of 'This file is screwed up somehow; maybe it's a 16 vs 32-bit
> problem?' I also can run them from a Windows command line instead of only
> from a cygwin command line. So that's hugely important, and a great sign.
>
> On the negative side on Windows, I still can't get it to build
> libtelicems. As noted in my last message, if I configure manually within
> cygwin, I get an error message, and if I run win32-dev-setup after
> manually updating setup-cellml-api.sh to include '--enable-telicems',
> everything runs, but the library is not created. I'm not sure how I can
> tell if it's being configured correctly and not being run, or what.

I think we may have regressed somewhat on the Windows build, since we
currently have technical problems with the build system - that is
something that should be sorted out early next year (we are waiting on
new hardware for a proper Windows build system) - I think the best first
step for Lucian is to get everything working well on POSIX systems, and
then look into the issues porting it to Windows.

>
> On UNIX, I can now successfully compile the cellml api with telicems
> enabled, and it creates libtelicems in cellml-api/.libs/ There are test
> files that are missing (as noted in my previous email) causing 'make' to
> fail, so I just went through the Makefile and deleted them; the result was
> that 'make' successfully created everything else. (While you're fixing
> things, 'make install' does not install libtelicems yet.)
>
> This lets me compile libantimony successfully, along with cellml2antimony
> and antimony2cellml. However, the former crashes (well, asserts) within a
> routine written for me by Andrew 'makeUTF16', designed to convert
> std::strings to wstrings. This is perhaps outside the purview of this
> group, but if anyone else ever uses the api in C++, they may well do the
> same thing, so or what it's worth, here's the output from running it
> within gdb:

I think that it is probably a downstream effect of some kind of memory
usage error earlier on corrupting things. I'd suggest running it through
valgrind memcheck which will probably find the original cause of the crash.

Best wishes,
Andrew

>
>
> -----------
> Starting program: /home/lpsmith/antimony/bin/cellml2antimony
> ~/CellML/models/adrian_chandler_hodgkin_1970/adrian_chandler_hodgkin_1970.cellml
> [Thread debugging using libthread_db enabled]
> cellml2antimony: malloc.c:3096: sYSMALLOc: Assertion `(old_top ==
> (((mbinptr) (((char *)&((av)->bins[((1) - 1) * 2])) - __builtin_offsetof
> (struct malloc_chunk, fd))))&& old_size == 0) || ((unsigned long)
> (old_size)>= (unsigned long)((((__builtin_offsetof (struct malloc_chunk,
> fd_nextsize))+((2 * (sizeof(size_t))) - 1))& ~((2 * (sizeof(size_t))) -
> 1)))&& ((old_top)->size& 0x1)&& ((unsigned long)old_end& pagemask) ==
> 0)' failed.
>
> Program received signal SIGABRT, Aborted.
> 0x0012d422 in __kernel_vsyscall ()
>
> (gdb) bt
> #0 0x0012d422 in __kernel_vsyscall ()
> #1 0x0080a651 in *__GI_raise (sig=6)
> at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
> #2 0x0080da82 in *__GI_abort () at abort.c:92
> #3 0x0084b794 in __malloc_assert (assertion=<value optimized out>,
> file=<value optimized out>, line=3096, function=0x912cd9 "sYSMALLOc")
> at malloc.c:352
> #4 0x0084e446 in sYSMALLOc (av=<value optimized out>,
> bytes=<value optimized out>) at malloc.c:3093
> #5 _int_malloc (av=<value optimized out>, bytes=<value optimized out>)
> at malloc.c:4746
> #6 0x0084ff9c in *__GI___libc_malloc (bytes=384) at malloc.c:3660
> #7 0x00762c07 in operator new(unsigned int) () from
> /usr/lib/libstdc++.so.6
> #8 0x00756cea in std::basic_string<wchar_t, std::char_traits<wchar_t>,
> std::allocator<wchar_t> >::_Rep::_S_create(unsigned int, unsigned int,
> std::allocator<wchar_t> const&) () from /usr/lib/libstdc++.so.6
> #9 0x00758594 in ?? () from /usr/lib/libstdc++.so.6
> #10 0x00758786 in std::basic_string<wchar_t, std::char_traits<wchar_t>,
> std::allocator<wchar_t> >::basic_string(wchar_t const*,
> std::allocator<wchar_t> const&)
> () from /usr/lib/libstdc++.so.6
> #11 0x080547c9 in makeUTF16 (aStr=...) at src/antimony_api.cpp:29
> #12 0x08056bab in loadCellMLFile (
> filename=0xbffff712
> "/home/lpsmith/CellML/models/adrian_chandler_hodgkin_1970/adrian_chandler_hodgkin_1970.cellml")
> at src/antimony_api.cpp:331
> #13 0x08053a84 in main (argc=2, argv=0xbffff594) at
> src/cellml2antimony.cpp:21
>
> (gdb) frame 11
> #11 0x080547c9 in makeUTF16 (aStr=...) at src/antimony_api.cpp:29
> 29 std::wstring s = buf;
>
> (gdb) l
> 24
> 25 std::wstring makeUTF16(const std::string& aStr)
> 26 {
> 27 wchar_t* buf = new wchar_t[aStr.length() + 1];
> 28 mbstowcs(buf, aStr.c_str(), aStr.length());
> 29 std::wstring s = buf;
> 30 delete [] buf;
> 31 return s;
> 32 }
>
> (gdb) p aStr
> $5 = (const std::string&) @0xbffff434: {static npos = 4294967295,
> _M_dataplus = {<std::allocator<char>> =
> {<__gnu_cxx::new_allocator<char>> = {<No data fields>},<No data fields>},
> _M_p = 0x8111d84
> "/home/lpsmith/CellML/models/adrian_chandler_hodgkin_1970/adrian_chandler_hodgkin_1970.cellml"}}
>
>
> -Lucian
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