<div dir="ltr">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 touch!</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 22, 2015 at 2:04 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On 21/09/15 19:52, Sabyasachi Sahoo wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs developers,<br>
<br>
I am a parallel programming researcher and would like to contribute to<br>
Gromacs molecular dynamics software by helping to nail down any<br>
bottlenecks that occur in scaling of the software on multiple CPUs (and<br>
probably improved performance in exa-scale era.) I am already in process<br>
of collecting profiling results to identify the phases that can be<br>
improved (and also for few other MD softwares).<br>
<br>
Hence, I would request all of you to please suggest me some possible<br>
areas of research, on which we can work on, for better scaling of<br>
Gromacs, (and/or MD softwares in general.) Going through the official<br>
website documentation helps me realise that implementing a truly<br>
parallel FFT (or making it scale better) in Gromacs will be truly<br>
helpful. The latest paper on Gromacs 5.0 concludes saying an algorithm<br>
implementing preempting fine grained tasks based on priority can lead to<br>
improvements. I am also trying to look into it and would want to know<br>
your take on this.<br>
<br>
You could also direct me to the link on the website, or any person<br>
concerned with this. You could also point me to any link in developer<br>
zone that I might have missed. Any more insight into matter will be<br>
really appreciated.<br>
<br>
</blockquote>
<br></span>
Have you looked at the source code so far? It can be a tad overwhelming although we're working on restructuring.<br>
<br>
You can follow the work in progress on our patch server:<br>
<a href="https://gerrit.gromacs.org/#/q/status:open" rel="noreferrer" target="_blank">https://gerrit.gromacs.org/#/q/status:open</a><div class="HOEnZb"><div class="h5"><br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks in advance.<br>
<br>
--<br>
Yours sincerely,<br>
Sabyasachi Sahoo<br>
Supercomputer Education & Research Center<br>
Indian Institute of Science - Bangalore<br>
<br>
<br>
</blockquote>
<br>
<br></div></div><span class="HOEnZb"><font color="#888888">
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" rel="noreferrer" target="_blank">http://folding.bmc.uu.se</a><br>
-- <br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr">Yours sincerely,<div>Sabyasachi Sahoo</div><div>M. Tech - Computational Science</div><div><div style="font-size:small">Supercomputer Education & Research Center<br></div><div style="font-size:small">Indian Institute of Science - Bangalore</div></div></div></div></div></div></div></div></div></div>
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