[gmx-developers] Parallelism in trajectory analysis tools

[David van der Spoel]

Den 2018-08-20 kl. 08:25, skrev Mark Abraham:
> Hi,
> 
> As Roland noted, there was some work done at ORNL. Teemu's original plan 
> embraced the possibility of parallel analysis, but there's no 
> implementation in master branch.
> 
> I don't have a clear picture of a use case that has enough need of 
> compute that the per-frame workload would not be dominated by overheads 
> from I/O and the analysis workflow runner. Peter Kasson suggested local 
> pressure some time (IIRC). Perhaps there are some goodness-of-fit 
> post-simulation analyses for SAXS/SANS/CryoEM that might motivate?

Simple things like RDF and Hbond can be very time consuming. It would 
not be hard to fix a few of these to use OpenMP of course. Is that to be 
preferred?

> 
> Mark
> 
> On Thu, Aug 9, 2018 at 4:46 PM Kutzner, Carsten <ckutzne at gwdg.de 
> <mailto:ckutzne at gwdg.de>> wrote:
> 
>     Hi,
> 
>     what is the status of using any type of parallelism to speed
>     up trajectory analysis tools?
> 
>     I guess OpenMP should be no problem, but what about MPI?
> 
>     What are the plans here / what would be preferred in future
>     patches?
> 
>     Thanks!
>        Carsten
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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