<div dir="ltr">Hi,<div><br></div><div>I too use -deffnm and would cry a little bit if it goes, but the problem is that the design is fundamentally broken and despite everybody really wanting it, keeping it will require serious effort to fix the broken aspects. For the last few years, we've all agreed that it's nice to have, and also agree that "somebody else" should fix it :-)</div><div><br></div><div>The problem has to do with modularization. In general, lots of places in GROMACS can write lots of different files, and exactly what files need to be written will depend on the module (some analysis tools might for instance like to write 3-4 different data or XVG files, and mdrun occasionally writes multiple xvg files too, e.g. for pulling).</div><div><br></div><div>The way deffnm currently works is to just set every single filename option to the default string, which means several output places will sometimes try to write files with identical names, and they will typically do so silently (which can be a disaster for long simulations where we they suddenly end up overwriting valuable data without warning).</div><div><br></div><div>To solve it, one would likely need to redesign an overall class to handle files & filenames in the input section, and then have other modules register with this both to get a preferred default filename, and/or decide whether things should be suffixed, etc. If automatic suffixes are added, that in turn might lead to other complications in places like checkpointing, since the string used in deffnm would not be the same as the filename, and one would have to decide how to handle that on checkpoint restarts, etc.</div><div><br></div><div><br></div><div>Thus, we can't really vote by only saying it would be useful, but the real votes are cast when all of us (me included) decide not to spend that effort :-)<br></div><div><br></div><div><br></div><div>I would still like to have it, but to me there are other higher-priority items that I'll spend my efforts on (e.g. removing the last C source files with new C++ SIMD kernels, new JSON-based file formats, task parallelism and making TNG solid).</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 4, 2018 at 10:35 AM, Jernej Zidar <span dir="ltr"><<a href="mailto:jernej.zidar@gmail.com" target="_blank">jernej.zidar@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>The "-deffnm" option is very handy because the user doesn't have to specify every single output file (energy, trajectory, log, checkpoint). This option should be kept if it is not too much trouble. Personally, I'd like to see this option applied to other tools as well (trjconv for example).</div><div><br></div><div>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. </div><div><br></div><div>Comments?</div><div> </div><div>Cheers,</div><div>Jernej Zidar<span class=""><br><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 4, 2018 at 5:15 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div>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.<br></div><div><br></div><div>Thanks,</div><div><br></div><div>Mark</div></div>
<br></blockquote></div></div></span></div></div>
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