[gmx-users] Rerun error - the file has been replaced or its content has been changed

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 9 21:12:36 CEST 2012

On 10/04/2012 5:07 AM, Steven Neumann wrote:
> Well, I did not change anything. I use Gromacs 4.5.4. Other windows 
> work fine, just 2 out of 30 failed like this. Shall I rerun it from 
> the begining then?

OK, I'll spell it out then... if your file system might have been 
transiently failing to serve a file, try the command again. Make a 
backup. Try the backup you may have created previously.

Do some detective work... what was the file size? when was it last 
modified? what size is it now? is 641K the whole file or just part of 
it? What can you deduce from all of this?


> On Mon, Apr 9, 2012 at 8:04 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 10/04/2012 4:50 AM, Steven Neumann wrote:
>         Dear Gmx Users,
>         I am running umbrella sampling on the cluster. The wall time
>         is 72 hours so I have to rerun my simulation every time. After
>         first 72 hours I rerun my simulation:
>         pbsexec mpiexec mdrun -s umbrella0.tpr -cpi umbrella0.cpt
>         -append -deffnm umbrella0 -pf pullf-umbrella0.xvg -px
>         pullx-umbrella0.xvg
>         where tpr file is the one used in the initial MD run. Then I got:
>         Fatal error:
>         Can't read 640794 bytes of 'pullx-umbrella0.xvg' to compute
>         checksum. The file has been replaced or its contents has been
>         modified.
>         Do you have any clue?
>     It means what it says. The files cannot change between runs if you
>     wish to use -append. It is possible your filesystem was
>     transiently failing to serve the correct file.
>     Mark
>     -- 
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