[gmx-users] Buffer overflow on Fedora 10

[David van der Spoel]

Adam Huffman wrote:
> Jussi Lehtola wrote:
>> On Mon, 2009-07-06 at 11:37 +0100, Adam Huffman wrote:
>>  
>>> 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
>>>     
>>
>> When I run
>> $ gdb g_mdrun
>> (gdb) r
>>
>> I get
>> (clip)
>> Program g_mdrun, VERSION 4.0.4
>> Source code file: ../../../src/gmxlib/gmxfio.c, line: 736
>>
>> Can not open file:
>> topol.tpr
>> (clip)
>> Program exited with code 0377.
>>   
> Yes, I see that.  At this stage, I just want the program to start 
> without crashing.  At the moment it crashes even without trying to load 
> any input files, but not when run under gdb.
If you are adventurous you could try to run it through valgrind which 
will spot memory errors.

valgrind mdrun [ options ]

You may need to install the valgrind program.

>>
>> Instead of running
>> $ gdb g_mdrun [mdrun options]
>> (gdb) run
>> you need to run
>> $ gdb g_mdrun
>> (gdb) run [mdrun options]
>>   
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
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