[gmx-developers] Prospective research areas of GROMACS

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 21 22:34:26 CEST 2015

On 21/09/15 19:52, Sabyasachi Sahoo wrote:
> Dear Gromacs developers,
> I am a parallel programming researcher and would like to contribute to
> Gromacs molecular dynamics software by helping to nail down any
> bottlenecks that occur in scaling of the software on multiple CPUs (and
> probably improved performance in exa-scale era.) I am already in process
> of collecting profiling results to identify the phases that can be
> improved (and also for few other MD softwares).
> Hence, I would request all of you to please suggest me some possible
> areas of research, on which we can work on, for better scaling of
> Gromacs, (and/or MD softwares in general.) Going through the official
> website documentation helps me realise that implementing a truly
> parallel FFT (or making it scale better) in Gromacs will be truly
> helpful. The latest paper on Gromacs 5.0 concludes saying an algorithm
> implementing preempting fine grained tasks based on priority can lead to
> improvements. I am also trying to look into it and would want to know
> your take on this.
> You could also direct me to the link on the website, or any person
> concerned with this. You could also point me to any link in developer
> zone that I might have missed. Any more insight into matter will be
> really appreciated.

Have you looked at the source code so far? It can be a tad overwhelming 
although we're working on restructuring.

You can follow the work in progress on our patch server:

> Thanks in advance.
> --
> Yours sincerely,
> Sabyasachi Sahoo
> Supercomputer Education & Research Center
> Indian Institute of Science - Bangalore

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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