[gmx-developers] Prospective research areas of GROMACS

Sabyasachi Sahoo ssahoo.iisc at gmail.com
Tue Sep 22 11:37:57 CEST 2015

I haven't given a thorough look at the source code yet. I would definitely
be happy to work on areas that generically can help scalable performances.
Also, thanks for the link to patch server. I will look into it ad get in

On Tue, Sep 22, 2015 at 2:04 AM, David van der Spoel <spoel at xray.bmc.uu.se>

> 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:
> https://gerrit.gromacs.org/#/q/status:open
> 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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Yours sincerely,
Sabyasachi Sahoo
M. Tech - Computational Science
Supercomputer Education & Research Center
Indian Institute of Science - Bangalore
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