[gmx-developers] Use of SVE in GROMACS

[Szilárd Páll]

Hi Guido,

Initial SVE support has just been merged a few days ago and will be
included in the 2021 release:
https://gitlab.com/gromacs/gromacs/-/merge_requests/553

This is initial support with a fixed implementation with some
optimizations for A64fx.

Your contributions are welcome! For the 2021 release, which will have
a beta release very soon, we can only accept minor improvements and
tweaks. After the release-2021 branch is forked, further development
should target the master branch.

See further replies below.

> 3)      Is this routine responsible only of the non-bonded forces? Does the “nb” prefix indicate “non-bonded”?

Yes.

> 4)      Is this same effect (“do_nb_verlet” the most expensive) measured for others benchmarks?

Yes. There are two possible exceptions:
- strong scaling where communication and other less algorithms that
scales less well than the nonbonded pair-interactions starts to
dominate;
- uncommon rare simulation types where other very high cost algorithms are used.

The former should become clear when you scale out to a few hundred
atoms/core. The latter I'd suggest to not worry about.

> 5)      Are there others ready-to-use and small benchmarks like the “ion_channel.tpr” available (<150K atoms)? Test Case B from UEABS (3.3 M atoms) is not suitable for my hardware resources.

You can use the "rnase" benchamrk systems 19k/24k atoms (see here
http://ftp.gromacs.org/benchmarks/).

You might also find useful the nonbonded-benchmark tool, see:
http://manual.gromacs.org/current/onlinehelp/gmx-nonbonded-benchmark.html

Let us know if you have further questions.

Cheers
--
Szilárd




>
> Thanks a lot, Guido.
>
>
>
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