[MINC-users] minctracc glibc error detected

[Vladimir S. Fonov]

No, that's not it - the example doesn't have long file names.

On 16-07-12 10:22 PM, Robert D. Vincent wrote:
> 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)
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>>
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