[gmx-developers] Fwd: renaming Gromacs binaries

Wed Jun 9 23:40:37 CEST 2010

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Thursday, June 10, 2010 7:28
Subject: Re: [gmx-developers] Fwd: renaming Gromacs binaries
To: Discussion list for GROMACS development <gmx-developers at gromacs.org>

> 
> 
> chris.neale at utoronto.ca wrote:
> >I haven't experienced any naming problems (is there really 
> another tool called grompp?), but I suppose that if people are, 
> then that is a strong argument in favour of changing the names.
> >
> 
> I would think that the more unique programs don't present a 
> problem, so avoiding renaming a bunch of essential programs 
> would be nice.  The bugzilla is complaining about programs 
> like luck, wheel, highway, etc.  Shouldn't the focus be on 
> those programs, such that the core programs that most users 
> employ for typical workflows simply be left alone?  I know 
> I wouldn't be hard pressed if luck all of a sudden became g_luck 
> - I don't tend to use these in any sort of scripts...or ever :)
> 
> Just my $0.02.  Maybe there really is a problem, but as 
> Chris said, are grompp, mdrun, etc. really getting in the way?

I like this suggestion. Move the problem executables now (to g_name, or the rubbish - what is highway good for?), and defer more far-reaching changes to 5.0. If grompp might be going away, per Erik's threat, then scripts will mostly be breaking anyway at that time.

Mark

> >The converse argument: I compile the gromacs that is used by a 
> number of people. Since I am aware of this name changing, I will 
> create my own links so that users can access files as they used 
> to. However, not all people who compile gromacs read this list 
> and could end up getting annoyed with the "why did my scripts 
> stop working?" emails that they are bound to get.
> >
> >Here's an example of how the non-existence of mdrun could spell 
> disaster (and did for me recently):
> >
> >STARTTIME=$(date +%s)
> >for((;;)); do
> >  THISTIME=$(date +%s)
> >  stoprunning=$(echo "(${THISTIME} - ${STARTTIME})/3600 > 
> 40"|bc -l)
> >  if((stoprunning)); then
> >    break
> >  fi
> >  cp md1.cpt backup_md1.cpt.${RANDOM}
> >
> >  mdrun -maxh 6 ...
> >  #analyze the .xtc
> >  #trjconv -dt 50 the .xtc
> >  #rm the original .xtc
> >done
> >
> >This is taken from a real script of mine that I really used to 
> accidentally crash a GPFS filesystem a few days ago. The cp 
> md1.cpt backup_md1.cpt.${RANDOM} line is intended to avoid 
> bugzilla 390.
> >
> >If the mdrun command doesn't work, then what you get is not 
> nice checkpointing and analysis on the fly, but instead you copy 
> the .cpt file to a new name every second or so for 40 hours. 
> Submit a few of these at once and the load is too much for the 
> filesystem to handle.
> >
> >So changing scripts should be easy, but the consequences are 
> not always obvious -- especially when many users use scripts 
> written by somebody else int heir group.
> >
> >Note: I got an email failure trying to send this a minute ago, 
> so I appologize if this is the second such email.
> >
> >Chris.
> >
> >Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
> >
> >>On 2010-06-09 01.50, hess at sbc.su.se wrote:
> >>>Hi,
> >>>
> >>>I agree with Erik on all points.
> >>>
> >>>I also agree on the preference for g_...
> >>>Not only because it is shorter, but also because this causes
> >>>the least changes.
> >>
> >>
> >>And what about those voices (Chris Neale, Peter Kasson) that are
> >>vehemently against changing names?
> >>
> >>There is one serious problem with changing names, and changing 
> all your
> >>scripts, and that is that it becomes difficult to compare to older
> >>versions of gromacs (unless you also change names of binaries 
> in old
> >>gromacs installations).
> >>
> >>I'm happy to provide a simple perl script for patching scripts 
> if that
> >>is of any comfort - personally I think that is the way to go.
> >>
> >>Chris, Peter, more comments?
> >>>
> >>>Berk
> >>>
> >>>
> >>>>Hi,
> >>>>
> >>>>I don't really have any super-strong opinion, since we 
> usually use AFS and
> >>>>have separate modules for versions, etc., However:
> >>>>
> >>>>1. We can have arbitrary prefix/suffix modifiers, but let's 
> not do
> >>>>anything more complex (that will be a pain to implement both 
> in autoconf
> >>>>and cmake)
> >>>>
> >>>>2. I'm a bit hesitant to do any large changes at this point, 
> since we're
> >>>>gearing up for some major rearrangements as soon as we've 
> pushed out the
> >>>>4.5 release. We might make grompp optional, use a new tool 
> for fixing up
> >>>>structures, merge/change analysis tools, and then it also 
> seems natural to
> >>>>decide on a new well-designed naming scheme at that point?
> >>>>
> >>>>3. Long-term, I think we need to decide: Either we have a 
> _small_ number
> >>>>of programs that get installed e.g. in /usr/local/bin, or a 
> larger number
> >>>>in a separate directory.
> >>>>
> >>>>4. If I had to choose, my preference would be towards g_XXX 
> right now...
> >>>>
> >>>>Cheers,
> >>>>
> >>>>Erik
> >>>>
> >>>>On Jun 8, 2010, at 7:35 PM, David van der Spoel wrote:
> >>>>
> >>>>>
> >>>>>
> >>>>>-------- Original Message --------
> >>>>>Subject: renaming Gromacs binaries
> >>>>>Date: Tue, 8 Jun 2010 08:00:57 -0700
> >>>>>From: Peter Kasson<kasson at gmail.com>
> >>>>>Reply-To: kasson at stanford.edu
> >>>>>To: David van der Spoel<spoel at xray.bmc.uu.se>
> >>>>>
> >>>>>Hi David,
> >>>>> I'd put in a strong vote for having an easy way to 
> maintain the
> >>>>>current naming scheme if desired (although it might not be the
> >>>>>default).  There are a lot of scripts out there that 
> will get broken,
> >>>>>etc...
> >>>>>
> >>>>>
> >>>>>Thanks,
> >>>>>--Peter
> >>>>>-- 
> >>>>>gmx-developers mailing list
> >>>>>gmx-developers at gromacs.org
> >>>>>http://lists.gromacs.org/mailman/listinfo/gmx-developers
> >>>>>Please don't post (un)subscribe requests to the list. Use 
> the www
> >>>>>interface or send it to gmx-developers-request at gromacs.org.
> >>>>>
> >>>>
> >>>>----------------------------------------------------------
> >>>>Erik Lindahl<lindahl at cbr.su.se>
> >>>>Professor, Computational Structural Biology
> >>>>Center for Biomembrane Research&  Swedish e-Science 
> Research Center
> >>>>Department of Biochemistry&  Biophysics, Stockholm University
> >>>>Tel: +468164675 Cell: +46703844534
> >>>>
> >>>>-- 
> >>>>gmx-developers mailing list
> >>>>gmx-developers at gromacs.org
> >>>>http://lists.gromacs.org/mailman/listinfo/gmx-developers
> >>>>Please don't post (un)subscribe requests to the list. Use the
> >>>>www interface or send it to gmx-developers-request at gromacs.org.
> >>>>
> >>>
> >>
> >>
> >>-- 
> >>David van der Spoel, Ph.D., Professor of Biology
> >>Dept. of Cell & Molec. Biol., Uppsala University.
> >>Box 596, 75124 Uppsala, Sweden. Phone:    
> +46184714205.>>spoel at xray.bmc.uu.se    
> http://folding.bmc.uu.se>>-- 
> >>gmx-developers mailing list
> >>gmx-developers at gromacs.org
> >>http://lists.gromacs.org/mailman/listinfo/gmx-developers
> >>Please don't post (un)subscribe requests to the list. Use the www
> >>interface or send it to gmx-developers-request at gromacs.org.
> >
> >
> >
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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