[gmx-developers] Fwd: renaming Gromacs binaries

[Sander Pronk]

Great! I've just committed the cmake updates to reflect this.

We're left with

grompp
mdrun
tpbconv
pdb2gmx
gmxdump
gmxcheck
ngmx
do_dssp
editconf
eneconv
genbox
genconf
genrestr
make_ndx
mk_angndx
trjcat
trjconv
trjorder
xpm2ps
genion

Note the sometimes inconsistent naming (mk_angndx and make_ndx; both not easily found among all binaries on most macs/linux systems that begin with 'make' or 'mk'). 

I'd suggest changing these too to have a g_ prefix (for example, to make gromacs tools easy to find using the shell's tab completion), but also to install (using symlinks or just by installing two binaries) the binaries with the old names for the time being. We could have tools that are invoked by their old name emit a warning:

WARNING: g_genbox was invoked as genbox. The binary with this name is obsolete and will be removed soon. Please update your scripts

Sander



On Jun 10, 2010, at 06:37 , David van der Spoel wrote:

> On 2010-06-10 00.10, Nicholas Breen wrote:
>> On Wed, Jun 09, 2010 at 05:27:04PM -0400, Justin A. Lemkul wrote:
>>> Just my $0.02.  Maybe there really is a problem, but as Chris said, are
>>> grompp, mdrun, etc. really getting in the way?
>> 
>>> From a distribution packaging perspective, the only other command that's been a
>> problem in Debian was genbox, which conflicted with an unrelated piece of
>> raytracing software using the same binary name.
>> 
>> 
> Previously mdrun used to be part of the RAID tools on linux boxes as well. Both mdrun and genbox fall under the category of programs that are being used in scripts a lot.
> 
> I have now picked the low hanging fruit and renamed some of the less used tools to g_XXX, and also kicked out some stuff that was obsolete (average, scrollw). I decided not to touch the configure stuff, too messy, at least in Peter's proposal.
> 
> The following programs were renamed:
> luck
> wheel
> protonate
> x2top
> showcol
> highhway
> sigeps
> anadock
> 
> e.g.
> g_highway -f $GMXDATA/gromacs/top/highway.dat
> 
> -- 
> 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
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