[gmx-users] Prospective research areas of GROMACS

Sabyasachi Sahoo ssahoo.iisc at gmail.com
Mon Sep 21 19:50:52 CEST 2015

Thanks for the suggestion!

On Mon, Sep 21, 2015 at 10:58 PM, David van der Spoel <spoel at xray.bmc.uu.se>

> On 21/09/15 19:09, Sabyasachi Sahoo wrote:
>> Dear Gromacs users and 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.
>> Thanks in advance.
>> You can start by reposting on the gmx-developers list.
> Quite a bit is going on, but surely someone will be able to point to
> something useful you could contribute.
> Welcome to the developer crew!
> --
> 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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Yours sincerely,
Sabyasachi Sahoo
M. Tech - Computational Science
Supercomputer Education & Research Center
Indian Institute of Science - Bangalore

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