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

[Dmytro Kovalskyy]

Hi there,

Gromacs explodes with new version of libc
                         :-)  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