[gmx-developers] Use of SVE in GROMACS

[Berk Hess]

Hi,

No, there is no such thing. Since quite a lot of different data goes in, 
that would require some work to set up.

Cheers,

Berk

On 2020-10-09 11:00, Guido Giuntoli wrote:
> Hi,
>
> I would like to add another question to my previous email. I have searched tests for the function nbnbx_kernel_cpu but I didn't found any. Just to be sure, is there any more simplified version of the non-bonded benchmark that just calls nbnbx_kernel_cpu with simple hardcoded input parameters?
>
> My problem is that with the simulators I cannot use too much time in the data structures initialization like it is done in "gmx nonbonded-benchmark" (each instruction executed is very expensive). It is preferable to have all data structures initialialized in memory and jump fast to the kernels in order to see how the simulator performs there.
>
> Best regards | Mit freundlichen Grüßen
>
> Guido Giuntoli
> Software Solution Architect for Advance Computing
>
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> -----Original Message-----
> From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of Szilárd Páll
> Sent: Wednesday, October 7, 2020 1:58 PM
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Cc: Matthias Gries <matthias.gries at huawei.com>; gromacs.org_gmx-developers at maillist.sys.kth.se
> Subject: Re: [gmx-developers] Use of SVE in GROMACS
>
> 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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