[gmx-users] gmx 3.3.2 explodes with libc.so.6

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 7 14:48:10 CET 2007


Dmytro Kovalskyy wrote:
> Hi there,
> 
> Gromacs explodes with new version of libc

Did you compile it yourself?
Could you please recompile it with
CFLAGS=-g
and try to debug it?

Which OS and compilers did tou use?

>                          :-)  G  R  O  M  A  C  S  (-:
> 
> *** buffer overflow detected ***: editconf terminated
> ======= Backtrace: =========
> /lib/libc.so.6(__chk_fail+0x44)[0xb7a4bb34]
> /lib/libc.so.6[0xb7a4aff7]
> /usr/lib/libgmx.so.4(get_libdir+0x2bc)[0xb7c1841c]
> /usr/lib/libgmx.so.4(low_libfn+0x1b2)[0xb7c18652]
> /usr/lib/libgmx.so.4(low_libopen+0x2c)[0xb7c1870c]
> /usr/lib/libgmx.so.4[0xb7c0ed28]
> /usr/lib/libgmx.so.4(bromacs+0x33)[0xb7c0f093]
> /usr/lib/libgmx.so.4(CopyRight+0x63)[0xb7c0f103]
> /usr/lib/libgmxana.so.4(gmx_editconf+0x151)[0xb7f6c901]
> editconf[0x80484c2]
> /lib/libc.so.6(__libc_start_main+0xdc)[0xb799505c]
> editconf[0x8048411]
> ======= Memory map: ========
> 08048000-08049000 r-xp 00000000 03:01 549330     /usr/bin/editconf
> 08049000-0804a000 rwxp 00000000 03:01 549330     /usr/bin/editconf
> 0804a000-0806b000 rwxp 0804a000 00:00 0          [heap]
> b7966000-b7970000 r-xp 00000000 03:01 2366571    /lib/libgcc_s.so.1
> b7970000-b7971000 rwxp 0000a000 03:01 2366571    /lib/libgcc_s.so.1
> b7971000-b7972000 rwxp b7971000 00:00 0
> b7972000-b7974000 r-xp 00000000 03:01 2366509    /lib/libdl-2.5.so
> b7974000-b7976000 rwxp 00001000 03:01 2366509    /lib/libdl-2.5.so
> b7976000-b7977000 rwxp b7976000 00:00 0
> b7977000-b797b000 r-xp 00000000 03:01 543574     /usr/lib/libXdmcp.so.6.0.0
> b797b000-b797c000 rwxp 00003000 03:01 543574     /usr/lib/libXdmcp.so.6.0.0
> b797c000-b797e000 r-xp 00000000 03:01 543576     /usr/lib/libXau.so.6.0.0
> b797e000-b797f000 rwxp 00001000 03:01 543576     /usr/lib/libXau.so.6.0.0
> b797f000-b7a9f000 r-xp 00000000 03:01 2366503    /lib/libc-2.5.so
> b7a9f000-b7aa0000 r-xp 0011f000 03:01 2366503    /lib/libc-2.5.so
> b7aa0000-b7aa2000 rwxp 00120000 03:01 2366503    /lib/libc-2.5.so
> b7aa2000-b7aa5000 rwxp b7aa2000 00:00 0
> b7aa5000-b7b8f000 r-xp 00000000 03:01 543578     /usr/lib/libX11.so.6.2.0
> b7b8f000-b7b93000 rwxp 000e9000 03:01 543578     /usr/lib/libX11.so.6.2.0
> b7b93000-b7ba7000 r-xp 00000000 03:01 543754     /usr/lib/libICE.so.6.3.0
> b7ba7000-b7ba8000 rwxp 00013000 03:01 543754     /usr/lib/libICE.so.6.3.0
> b7ba8000-b7bab000 rwxp b7ba8000 00:00 0
> b7bab000-b7bb2000 r-xp 00000000 03:01 543756     /usr/lib/libSM.so.6.0.0
> b7bb2000-b7bb3000 rwxp 00006000 03:01 543756     /usr/lib/libSM.so.6.0.0
> b7bb3000-b7bd7000 r-xp 00000000 03:01 2366511    /lib/libm-2.5.so
> b7bd7000-b7bd9000 rwxp 00023000 03:01 2366511    /lib/libm-2.5.so
> b7bd9000-b7bea000 r-xp 00000000 03:01 2366513    /lib/libnsl-2.5.so
> b7bea000-b7bec000 rwxp 00011000 03:01 2366513    /lib/libnsl-2.5.so
> b7bec000-b7bee000 rwxp b7bec000 00:00 0
> b7bee000-b7da2000 r-xp 00000000 03:01 549411     /usr/lib/libgmx.so.4.0.0
> b7da2000-b7dab000 rwxp 001b3000 03:01 549411     /usr/lib/libgmx.so.4.0.0
> b7dab000-b7db0000 rwxp b7dab000 00:00 0
> b7db0000-b7ec5000 r-xp 00000000 03:01 549415     /usr/lib/libmd.so.4.0.0
> b7ec5000-b7ec6000 rwxp 00114000 03:01 549415     /usr/lib/libmd.so.4.0.0
> b7ec6000-b7ec7000 rwxp b7ec6000 00:00 0
> b7ec7000-b7fb0000 r-xp 00000000 03:01 549413     /usr/lib/libgmxana.so.4.0.0
> b7fb0000-b7fb7000 rwxp 000e8000 03:01 549413     /usr/lib/libgmxana.so.4.0.0
> b7fb7000-b7fb9000 rwxp b7fb7000 00:00 0
> b7fd2000-b7fd3000 r-xp b7fd2000 00:00 0          [vdso]
> b7fd3000-b7fea000 r-xp 00000000 03:01 2366497    /lib/ld-2.5.so
> b7fea000-b7fec000 rwxp 00016000 03:01 2366497    /lib/ld-2.5.so
> bfd84000-bfd98000 rwxp bfd84000 00:00 0          [stack]
> bfd98000-bfd99000 rw-p bfd98000 00:00 0
> 
> 
> [dikov at violet tmp]$ rpm -qf /lib/libc.so.6
> glibc-core-2.5-alt4
> 
> 
> Any ideas?
> 
> Dima
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se



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