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

[Dimitar Pachov]

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.

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

Thanks,
Dimitar
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110603/376adf40/attachment.html>