[gmx-users] Why does the -append option exist?

[Amit Choubey]

Well sometimes i run out of walltime when doing long simulations and append
helps me not to do any file management after restarting simulations from the
previous checkpoint.

On Fri, Jun 3, 2011 at 3:26 PM, Dimitar Pachov <dpachov at brandeis.edu> wrote:

>
> At first, I thought the -append option of the mdrun command was great.
> However, I don't think it is anymore and have actually  started questioning
> myself why it exists at the first place, and second, why has it become the
> default option in the newest versions?
>
> It is useless unless you run your simulations in a 100% safe from any
> unexpected problems (hardware, restarts, etc) mode, which is never the case.
> It is beyond me how such an option can become the default and how a
> statement like this:
>
> "By default the output will be appending to the existing output files. The
> checkpoint file contains checksums of all output files, such that *you
> will never loose data when some output files are modified, corrupt or
> removed.*"
>
> can be claimed without testing ALL of the scenarios that can lead to
> problems, that is, lost data.
>
> If one uses that option and the run is restarted and is again restarted
> before reaching the point of attempting to write a file, then things are
> lost, and most importantly, the most important piece of data, that being the
> trajectory file, could be completely lost! I don't know the code behind the
> checkpointing & appending, but I can see how easy one can overwrite 100ns
> trajectories, for example, and "obtain" the same trajectories of size ....
> 0.
>


Two restarts within a time frame where trajectory file is updated doesnt
make sense. I really dont understand how you can loose trajectory files.


> Using the checkpoint capability & appending make sense when many restarts
> are expected, but unfortunately it is exactly then when these options
> completely fail!
>

How ?


> As a new user of Gromacs, I must say I am disappointed, and would like to
> obtain an explanation of why the usage of these options is clearly stated to
> be safe when it is not, and why the append option is the default, and why at
> least a single warning has not been posted anywhere in the docs & manuals?
>

Use -noappend

>
> Thanks,
> Dimitar
>
>
>
>
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