[gmx-users] Buffer overflow on Fedora 10

Adam Huffman adam.huffman at gmail.com
Mon Jul 6 12:37:08 CEST 2009


Jussi Lehtola wrote:
> On Mon, 2009-07-06 at 11:18 +0100, Adam Huffman wrote:
>   
>> 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:
>>     
>
>   
>> 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.
>>     
>
> Install the debuginfo with
> # debuginfo-install gromacs
>
> and run gromacs with gdb:
> $ gdb g_mdrun
> (gdb) run -s topol.tpr (and so on.)
>
> Gdb might tell you to install the debuginfo of other packages too.
>
> I have been working on getting also debug binaries in the package, but I
> won't push the new package until 4.0.6 is released which fixes the build
> error on ppc64 architecture.
>   

I've installed several debuginfo packages and when run via gdb the crash 
doesn't occur...:

(gdb) r
Starting program: /usr/bin/g_mdrun
warning: "/usr/lib/debug/usr/lib64/atlas/libblas.so.3.0.debug": The 
separate debug info file has no debug info
warning: "/usr/lib/debug/usr/lib64/atlas/liblapack.so.3.0.debug": The 
separate debug info file has no debug info
[Thread debugging using libthread_db enabled]

then the usage message and

Program exited with code 0377.





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