[gmx-developers] functionality to deprecate in 2018 release

Mark Abraham mark.j.abraham at gmail.com
Thu Jan 4 10:55:49 CET 2018


On Thu, Jan 4, 2018 at 10:36 AM Jernej Zidar <jernej.zidar at gmail.com> wrote:

> Hi,
> The "-deffnm" option is very handy because the user doesn't have to
> specify every single output file (energy, trajectory, log, checkpoint).

But what's the requirement for renaming them? The default names are fine -
name collisions only arise when someone tries to do their entire
(sub)project in the same directory, which IMO is an anti-pattern.

> This option should be kept if it is not too much trouble.

The trouble is not the simple case, where it works fine. The trouble is the
forest of files that get written by all the modules. There's a lot of
infrastructure (and test cases) needed so that all combinations of e.g.
mdrun -deffnm -multi -px -append work reliably, now, and under maintenance.

Personally, I'd like to see this option applied to other tools as well
> (trjconv for example).

What's an example use case, please?

One suggestion: Would it be possible to have all the tools that analyze
> trajectories aware of the "-tu" switch ? It's way more convenient to
> specify the time in ns, ms, ... than in number of steps.

Maybe, but perhaps you are referring to -b and -t (which take input in ps,
not steps). Again, there's a lot of infrastructure and testing needed to
make that work (and potentially confusing if any other time-related option
is not also similarly customizable). We've historically done a poor job of
that, and now have about as much debt as assets... I don't see enough value

gmx tool -tu ns -b 10 -e 20


gmx tool -b 10000 -e 20000

for someone to want to put their time into it.


> Comments?
> Cheers,
> Jernej Zidar
> On Thu, Jan 4, 2018 at 5:15 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>> We should also be aware that -deffnm is brittle in the same way that
>> -multi is, because our filename-handling machinery doesn't centralize
>> changing the prefix/suffix needed to support -deffnm or -multi. So I think
>> we should plan to announce -deffnm as deprecated in the 2019 release (and
>> remove after that). If we think that's useful enough to want to keep, we
>> need people to put up their hands for the work to make all the mdrun
>> modules work with it.
>> Thanks,
>> Mark
>> --
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