[gmx-developers] functionality to deprecate in 2018 release

[Mark Abraham]

Hi,

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
in

gmx tool -tu ns -b 10 -e 20

vs

gmx tool -b 10000 -e 20000

for someone to want to put their time into it.

Mark


>
> 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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