Re: [AMBER-Developers] ioutfm = 0

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 26 Feb 2016 21:43:42 -0800

> On Feb 26, 2016, at 9:40 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Sat, Feb 27, 2016 at 12:24 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> Never mind, I think you meant to reply to Gerald but actually quoted me.
>>
>
> ‚ÄčI was anticipating the argument that you would only have to store *one*
> uncompressed ASCII trajectory at a time (since you'd compress before
> writing another one), so you'd still get net savings in disk space. But
> you pay for that disk space savings by sacrificing data (and in some cases,
> trajectory integrity).
>
> Your point is certainly valid that Amber can't write compressed ASCII
> trajectories directly (cpptraj can :)). All told, the benefits of ioutfm=1
> *far* outweigh the benefits of ioutfm=0. ioutfm=1 is a much more sensible
> default.

Is there any real benefit we could gain from compressed netcdf trajectories? (and restarts)? in pmemd. I am guessing they don't compress much but it might help on performance on systems with slow disk access? - Also is there support for writing netcdf files in parallel? We could 'potentially' avoid a coordinate reduction if we could write out in parallel but still get a single coherent netcdf file.

All the best
Ross

/\
\/
|\oss Walker

---------------------------------------------------------
| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| http://www.rosswalker.co.uk | http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Feb 26 2016 - 22:00:04 PST
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