[gmx-users] mdrun cannot append to file larger than 2Gb

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 26 19:08:55 CET 2011

Warren Gallin wrote:
> Hi,
> Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and got an error that I have never seen before, to whit:
> Program mdrun_mpi, VERSION 4.5.3
> Source code file: /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: 1727
> Fatal error:
> The original run wrote a file called 'traj.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've never had a problem with extending runs like this before.
> As suggested, I then ran with -noappend set, and it ran fine, creating a new set of numbered files for the ouput.  I am assuming that I'll be able to combine the trajectory files at the end of the process.


> Have I missed some fine point in compiling that has left mdrun a little broken?

Possibly, but it probably depends more on your system's architecture than 
anything you did.  There is a configure option --disable-largefile (which should 
be the default), so you'd have to check config.log to see if this was changed to 
--enable-largefile based on what the configuration script found.  Or you can 
re-compile and see if configuration fails with --enable-largefile and understand 
the reason.


> Thanks,
> Warren Gallin-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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