[gmx-users] Buffer overflow on Fedora 10

[Adam Huffman]

I have an odd problem running the Gromacs 4.0.4 RPM installable as part 
of Fedora 10.  On two machines, it runs fine.  On a third, each program 
I invoke dies as a result of the buffer overflow detector in glibc.  
Here's some example output:

 g_mdrun
                         :-)  G  R  O  M  A  C  S  (-:

*** buffer overflow detected ***: g_mdrun terminated
======= Backtrace: =========
/lib64/libc.so.6(__fortify_fail+0x37)[0x3a400ff4c7]
/lib64/libc.so.6[0x3a400fd370]
/lib64/libc.so.6[0x3a400fc15d]
/usr/lib64/libgmx.so.5(get_libdir+0x23f)[0x7fb3ac50e22f]
/usr/lib64/libgmx.so.5(low_libfn+0x1b4)[0x7fb3ac50e454]
/usr/lib64/libgmx.so.5(low_libopen+0x15)[0x7fb3ac50e4c5]
/usr/lib64/libgmx.so.5[0x7fb3ac5046d9]
/usr/lib64/libgmx.so.5(bromacs+0x21)[0x7fb3ac504931]
/usr/lib64/libgmx.so.5(CopyRight+0x59)[0x7fb3ac504999]
g_mdrun[0x4153b7]
/lib64/libc.so.6(__libc_start_main+0xe6)[0x3a4001e576]
g_mdrun[0x404539]
======= Memory map: ========
00400000-0041f000 r-xp 00000000 fd:02 2723129                            
/usr/bin/g_mdrun
0061f000-00621000 rw-p 0001f000 fd:02 2723129                            
/usr/bin/g_mdrun
025c9000-025ea000 rw-p 025c9000 00:00 0                                  
[heap]
3a3ec00000-3a3ec20000 r-xp 00000000 08:06 1114115                        
/lib64/ld-2.9.so
3a3ee1f000-3a3ee20000 r--p 0001f000 08:06 1114115                        
/lib64/ld-2.9.so
3a3ee20000-3a3ee21000 rw-p 00020000 08:06 1114115                        
/lib64/ld-2.9.so
3a3f000000-3a3f0f1000 r-xp 00000000 fd:02 2426042                        
/usr/lib64/libfftw3f.so.3.2.3
3a3f0f1000-3a3f2f1000 ---p 000f1000 fd:02 2426042                        
/usr/lib64/libfftw3f.so.3.2.3
3a3f2f1000-3a3f2f8000 rw-p 000f1000 fd:02 2426042                        
/usr/lib64/libfftw3f.so.3.2.3
3a40000000-3a40168000 r-xp 00000000 08:06 1114117                        
/lib64/libc-2.9.so
3a40168000-3a40368000 ---p 00168000 08:06 1114117                        
/lib64/libc-2.9.so
3a40368000-3a4036c000 r--p 00168000 08:06 1114117                        
/lib64/libc-2.9.so
3a4036c000-3a4036d000 rw-p 0016c000 08:06 1114117                        
/lib64/libc-2.9.so
3a4036d000-3a40372000 rw-p 3a4036d000 00:00 0
3a40400000-3a40484000 r-xp 00000000 08:06 1114123                        
/lib64/libm-2.9.so
3a40484000-3a40683000 ---p 00084000 08:06 1114123                        
/lib64/libm-2.9.so
3a40683000-3a40684000 r--p 00083000 08:06 1114123                        
/lib64/libm-2.9.so
3a40684000-3a40685000 rw-p 00084000 08:06 1114123                        
/lib64/libm-2.9.so
3a40800000-3a40802000 r-xp 00000000 08:06 1114125                        
/lib64/libdl-2.9.so
3a40802000-3a40a02000 ---p 00002000 08:06 1114125                        
/lib64/libdl-2.9.so
3a40a02000-3a40a03000 r--p 00002000 08:06 1114125                        
/lib64/libdl-2.9.so
3a40a03000-3a40a04000 rw-p 00003000 08:06 1114125                        
/lib64/libdl-2.9.so
3a40c00000-3a40c17000 r-xp 00000000 08:06 1114136                        
/lib64/libpthread-2.9.so
3a40c17000-3a40e16000 ---p 00017000 08:06 1114136                        
/lib64/libpthread-2.9.so
3a40e16000-3a40e17000 r--p 00016000 08:06 1114136                        
/lib64/libpthread-2.9.so
3a40e17000-3a40e18000 rw-p 00017000 08:06 1114136                        
/lib64/libpthread-2.9.so
3a40e18000-3a40e1c000 rw-p 3a40e18000 00:00 0
3a41000000-3a41015000 r-xp 00000000 08:06 1114139                        
/lib64/libz.so.1.2.3
3a41015000-3a41214000 ---p 00015000 08:06 1114139                        
/lib64/libz.so.1.2.3
3a41214000-3a41215000 rw-p 00014000 08:06 1114139                        
/lib64/libz.so.1.2.3
3a41800000-3a41802000 r-xp 00000000 fd:02 2425045                        
/usr/lib64/libXau.so.6.0.0
3a41802000-3a41a01000 ---p 00002000 fd:02 2425045                        
/usr/lib64/libXau.so.6.0.0
3a41a01000-3a41a02000 rw-p 00001000 fd:02 2425045                        
/usr/lib64/libXau.so.6.0.0
3a41c00000-3a41c05000 r-xp 00000000 fd:02 2425032                        
/usr/lib64/libXdmcp.so.6.0.0
3a41c05000-3a41e04000 ---p 00005000 fd:02 2425032                        
/usr/lib64/libXdmcp.so.6.0.0
3a41e04000-3a41e05000 rw-p 00004000 fd:02 2425032                        
/usr/lib64/libXdmcp.so.6.0.0
3a42000000-3a42105000 r-xp 00000000 fd:02 2425062                        
/usr/lib64/libX11.so.6.2.0
3a42105000-3a42305000 ---p 00105000 fd:02 2425062                        
/usr/lib64/libX11.so.6.2.0
3a42305000-3a4230b000 rw-p 00105000 fd:02 2425062                        
/usr/lib64/libX11.so.6.2.0
3a43400000-3a43403000 r-xp 00000000 08:06 1114147                        
/lib64/libuuid.so.1.2
3a43403000-3a43603000 ---p 00003000 08:06 1114147                        
/lib64/libuuid.so.1.2
3a43603000-3a43604000 rw-p 00003000 08:06 1114147                        
/lib64/libuuid.so.1.2
3a43800000-3a43817000 r-xp 00000000 fd:02 2425041                        
/usr/lib64/libICE.so.6.3.0
3a43817000-3a43a16000 ---p 00017000 fd:02 2425041                        
/usr/lib64/libICE.so.6.3.0
3a43a16000-3a43a18000 rw-p 00016000 fd:02 2425041                        
/usr/lib64/libICE.so.6.3.0
3a43a18000-3a43a1b000 rw-p 3a43a18000 00:00 0
3a43c00000-3a43c08000 r-xp 00000000 fd:02 2425029                        
/usr/lib64/libSM.so.6.0.0
3a43c08000-3a43e07000 ---p 00008000 fd:02 2425029                        
/usr/lib64/libSM.so.6.0.0
3a43e07000-3a43e08000 rw-p 00007000 fd:02 2425029                        
/usr/lib64/libSM.so.6.0.0
3a44000000-3a44016000 r-xp 0000Aborted

The same thing happens if I recompile the SRPM myself and install that.

Any clues as to how to track this down would be greatly appreciated.

Adam