[gmx-users] mdrun did not support large file offsets

[Justin A. Lemkul]

Bert wrote:
> Dear gmx-users,
> 
>    When I continued a run on my x86_64 linux clusters using the command
> "mdrun -deffnm prod -cpi prod.cpt -append", I got the errors as below:
> 
> Program mdrun, VERSION 4.5.4
> Source code file: checkpoint.c, line: 1734
> Fatal error:
> The original run wrote a file called 'prod.xtc' which is larger than 2 GB,
> but mdrun did not support large file offsets. Can not append. Run mdrun with
> -noappend
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 
> I also tried to recompile gromacs with alternative option
> --enable-largefile, but it still could not work. Then I compared the
> config.log generated using --enable-largefile and --disable-largefile
> (default) after configured, however, the two files were almost the same.
> 
> How to solve this problem? Any suggestions are appreciated. Thanks in
> advance.
> 

The error message gives you the solution. Use the -noappend option and 
concatenate your output files later.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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