Hello,
I've been able to replicate this behavior on our systems,
it appears to be for 32-bit centos binaries only, and occurs just
before the binary exits, but after the results have been written to
file. Any results you get from the analysis should be fine - we're
investigating the cause of the segmentation fault.
Many Regards
Matthew
> Dear folks,
>
> I've replaced my old FSL 4.1.2 with 4.1.3(centos5_32), and I used SGE
> to do parallel computing (four Ubuntu 8.04.2 nodes and one Centos 5.3
> node). When I tried one higher level analysis, I got core dump files
> in copeN.feat dir and error log in flameo computiion as below:
> -------------------------------------------------------------------
> /opt/fsl/bin/flameo --cope=tmpcope0000 --vc=tmpvarcope0000
> --dvc=tmptdof0000 --mask=tmpmask0000 --ld=stats0000 --dm=design.mat
> --cs=design.grp --tc=design.con --io --runmode=flame1
> *** glibc detected *** /opt/fsl/bin/flameo: free(): invalid pointer:
> 0x00cb4000 ***
> ======= Backtrace: =========
> /lib/libc.so.6[0xbdf0f1]
> /lib/libc.so.6(cfree+0x90)[0xbe2bc0]
> /usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0x5538571]
> /opt/fsl/bin/flameo[0x8080038]
> /opt/fsl/bin/flameo[0x80809b0]
> /opt/fsl/bin/flameo[0x807ede6]
> /lib/libc.so.6(__libc_start_main+0xdc)[0xb8be8c]
> /opt/fsl/bin/flameo(__gxx_personality_v0+0x105)[0x804afb1]
> ======= Memory map: ========
> 00193000-0019e000 r-xp 00000000 08:06 518681
> /lib/libgcc_s-4.1.2-20080825.so.1
> 0019e000-0019f000 rwxp 0000a000 08:06 518681
> /lib/libgcc_s-4.1.2-20080825.so.1
> 001a6000-001c0000 r-xp 00000000 08:06 518674 /lib/ld-2.5.so
> 001c0000-001c1000 r-xp 00019000 08:06 518674 /lib/ld-2.5.so
> 001c1000-001c2000 rwxp 0001a000 08:06 518674 /lib/ld-2.5.so
> 00b76000-00cb4000 r-xp 00000000 08:06 518675 /lib/libc-2.5.so
> 00cb4000-00cb6000 r-xp 0013e000 08:06 518675 /lib/libc-2.5.so
> 00cb6000-00cb7000 rwxp 00140000 08:06 518675 /lib/libc-2.5.so
> 00cb7000-00cba000 rwxp 00cb7000 00:00 0
> 00cbc000-00ce1000 r-xp 00000000 08:06 518678 /lib/libm-2.5.so
> 00ce1000-00ce2000 r-xp 00024000 08:06 518678 /lib/libm-2.5.so
> 00ce2000-00ce3000 rwxp 00025000 08:06 518678 /lib/libm-2.5.so
> 05485000-05565000 r-xp 00000000 08:05 6264673 /usr/lib/libstdc+
> +.so.6.0.8
> 05565000-05569000 r-xp 000df000 08:05 6264673 /usr/lib/libstdc+
> +.so.6.0.8
> 05569000-0556a000 rwxp 000e3000 08:05 6264673 /usr/lib/libstdc+
> +.so.6.0.8
> 0556a000-05570000 rwxp 0556a000 00:00 0
> 08048000-08215000 r-xp 00000000 00:1b 7252112 /opt/fsl/bin/flameo
> 08215000-08216000 rwxp 001cd000 00:1b 7252112 /opt/fsl/bin/flameo
> 085fc000-08be4000 rwxp 085fc000 00:00 0
> 40000000-40001000 r-xp 40000000 00:00 0 [vdso]
> 40001000-40003000 rwxp 40001000 00:00 0
> 4001a000-4001b000 rwxp 4001a000 00:00 0
> 40100000-40121000 rwxp 40100000 00:00 0
> 40121000-40200000 ---p 40121000 00:00 0
> bfd6c000-bfd83000 rw-p bfd6c000 00:00 0 [stack]
> ------------------------------------------------------------------
>
> But, I could see that flameo was doing its job:
> ------------------------------------------------------------------
> Log directory is: stats0000
> ...
> ------------------------------------------------------------------
>
> I also tried the 4.1.3 for centos4_32, I got ont core file in
> copeN.feat and error log as below:
> ------------------------------------------------------------------
> /opt/fsl/bin/flameo --cope=tmpcope0000 --vc=tmpvarcope0000
> --dvc=tmptdof0000 --mask=tmpmask0000 --ld=stats0000 --dm=design.mat
> --cs=design.grp --tc=design.con --io --runmode=flame1
> Segmentation fault (core dumped)
> Segmentation fault (core dumped)
> ...
> ------------------------------------------------------------------
> Still, I could see "Log directory is: stats0000"
>
> I tried two times for the two version above, and the error is
> reproducable. When I switched back to 4.1.2, it became normal.
>
> Is it a bug? or something like that?
>
> --
> Best Regards
>
>
> National Key Laboratory of Cognitive Neuroscience and Learning
> Beijing Normal University
> Beijing, China. 100875
> Tel: +86-13811953774
> web: http://psychbrain.bnu.edu.cn
> ==============================================
> Welcome to MuDuo JinSheng BBS @ Beijing Normal University
> telnet://bbs.mdjs.org
> http://bbs.mdjs.org
>
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