Tom -
The suffix only applies to output files, not mdin, prmtop, inpcrd or refc.
I find this sort of thing useful in linking all the associated output
together, though obviously you can solve the problem via scripting too.
However, with -suffix, then you can do it all in two spots - you increment
the suffix, and apply the last suffix value to your restrt. Furthermore,
you don't have to keep track of which outputs you actually requested; they
will all get tagged the same way. It is not a huge deal, but I put it in
pmemd because it saves me a ton of typing on the ~20 different systems I
am
running on testing, benchmarking, and occasionally even collecting data.
Regards - Bob
----- Original Message -----
From: "Thomas Cheatham" <cheatham.chpc.utah.edu>
To: <amber-developers.scripps.edu>
Sent: Thursday, February 09, 2006 9:58 PM
Subject: Re: amber-developers: -suffix option for sander?
>
>> > 4) a new -suffix command line option. If you put -suffix
>> > 020906.1.4proc
>> > in the command line, then all the output files will have this
appended
>> > to
>> > the default name unless you explicitly specified a name for them on
the
>> > command line. So this applies to mdout, mdinfo, mden, mdcrd, mdvel,
>> > restrt, and logfile (pmemd now permits logfile naming also with a -l
>> > flag).
>> > This is a really simple, easy-to-use command line interface
enhancement
>> > you
>> > all may want to pick up for sander. The code is in get_cmdline.fpp
for
>> > pmemd.
>>
>> It sounds like a nice idea to me--it would get us a long way towards
>> having
>> a more standardized file nomenclature. I'm just posting this to the
>> developers' list to see if people have either objections or better
ideas
>> along
>> this line.
>
> I like this idea in some respect, but most likely would not use it in
> general. As I run now, I do:
>
> set pre = 1;
> set cur = 2;
>
> sander -O -c restrt.$pre -o mdout.$cur -i mdin -p prmtop -r
> restrt.$cur -x traj.$cur
>
> and then update the script to increment $pre and $cur.
>
> The -suffix option doesn't help me in this case since (1) both the
prmtop
> and mdin files do not need a suffix as the same files are typically used
> throughout a long series of runs (i.e. I don't want to have to move the
> mdin and prmtop files to prmtop.suffix/mdin.suffix every run as I update
> suffix), and (2) I would have to move the previous restrt to the new
> inpcrd.suffix; so, I do not see a significant benefit for my usage
> pattern.
>
> I would happily use -prefix though! This would be advantageous for
> multisander since I could for each instance use the default names and
give
> each a different sub-directory for the files via -prefix ...
>
> --tom
>
> (p.s. DAC, ptraj in the tree was -DBINTRAJ wrapped and I'll get on final
> NetCDF mods, cluster + docs next week)
>
>
Received on Wed Apr 05 2006 - 23:49:42 PDT
