[MINC-users] minctracc glibc error detected

[Robert D. Vincent]

Hi,

I can't be certain, but looking through the git history I see at least one
possibility:

https://github.com/BIC-MNI/mni_autoreg/issues/7

    -bert


On Tue, Jul 12, 2016 at 4:23 PM, Mishkin Derakhshan <mishkind at gmail.com>
wrote:

> Aloha,
>
> For reasons I won't get into here, I am using an older version of minctracc
>
> mni-autoreg version 0.99.2
> $ minctracc -version
> The program <minctracc> was built from:
> Package mni_autoreg 0.99.2, compiled by rotor at romeo (i686-pc-linux-gnu) on
> Mon May  8 23:16:34 EDT 2006
>
> minc version 1.4
> $ mincinfo -version
> program: 1.4
> libminc: 1.4
> netcdf : 3.6.1 of May 11 2015 21:32:07 $
>
>
> The problem is that *sometimes* I get core dumps, i.e., on some subjects
> but not all. From what I can google from the error, I'm guessing it is an
> array out of bounds issue, and I'm also going to guess this was fixed in a
> later release of mni-autoreg or minc. Can anyone point me in the right
> direction. I'm hoping that maybe I can apply a small patch to minctracc in
> 0.99.2, recompile it, and then still have a version of minctracc that
> produces the same results as 0.99.2 in the cases where it doesn't fail.
>
> Mahalo,
> mishkin
>
> Here is a sample command line:
> minctracc stx_brain.mnc.gz stx.mnc.gz -model_mask stx_brain_mask.mnc.gz
> -transformation stx_analyze2minc_res.xfm -measure stx_brain_xfm_eval.txt
> -clobber
>
> Here is the default error/output:
> *** glibc detected *** free(): invalid next size (normal): 0x080e0808 ***
>
> Here is the debugging output:
> *** glibc detected *** minctracc: free(): invalid next size (normal):
> 0x08e9e560 ***
> ======= Backtrace: =========
> /lib/libc.so.6(+0x70c91)[0x55657c91]
> /lib/libc.so.6(+0x736f1)[0x5565a6f1]
> minctracc[0x80a3ea8]
> minctracc[0x80501af]
> minctracc[0x8051461]
> minctracc[0x8053e8c]
> minctracc[0x804c06a]
> /lib/libc.so.6(__libc_start_main+0xe6)[0x555fdd26]
> minctracc[0x8049881]
> ======= Memory map: ========
> 08048000-080d5000 r-xp 00000000 00:13 52030078
> minctracc
> 080d5000-080d8000 rw-p 0008d000 00:13 52030078
>  minctracc
> 080d8000-080da000 rw-p 00000000 00:00 0
> 08e96000-08eee000 rw-p 00000000 00:00 0
>  [heap]
> 55555000-55573000 r-xp 00000000 fd:01 18326
>  /lib/ld-2.12.so
> 55573000-55574000 r--p 0001e000 fd:01 18326
>  /lib/ld-2.12.so
> 55574000-55575000 rw-p 0001f000 fd:01 18326
>  /lib/ld-2.12.so
> 55575000-55576000 r-xp 00000000 00:00 0
>  [vdso]
> 55576000-55577000 rw-p 00000000 00:00 0
> 55577000-555ab000 r-xp 00000000 00:13 51884124
> libnetcdf.so.3.6.1
> 555ab000-555ac000 rw-p 00034000 00:13 51884124
> libnetcdf.so.3.6.1
> 555ac000-555af000 rw-p 00000000 00:00 0
> 555bd000-555e5000 r-xp 00000000 fd:01 15234
>  /lib/libm-2.12.so
> 555e5000-555e6000 r--p 00027000 fd:01 15234
>  /lib/libm-2.12.so
> 555e6000-555e7000 rw-p 00028000 fd:01 15234
>  /lib/libm-2.12.so
> 555e7000-55778000 r-xp 00000000 fd:01 3460
> /lib/libc-2.12.so
> 55778000-55779000 ---p 00191000 fd:01 3460
> /lib/libc-2.12.so
> 55779000-5577b000 r--p 00191000 fd:01 3460
> /lib/libc-2.12.so
> 5577b000-5577c000 rw-p 00193000 fd:01 3460
> /lib/libc-2.12.so
> 5577c000-56e45000 rw-p 00000000 00:00 0
> 56e55000-56e72000 r-xp 00000000 fd:01 12959
>  /lib/libgcc_s-4.4.7-20120601.so.1
> 56e72000-56e73000 rw-p 0001d000 fd:01 12959
>  /lib/libgcc_s-4.4.7-20120601.so.1
> 56f00000-56f21000 rw-p 00000000 00:00 0
> 56f21000-57000000 ---p 00000000 00:00 0
> ffbfd000-ffc13000 rw-p 00000000 00:00 0
>  [stack]
> Abort (core dumped)
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>