[gmx-developers] PME on GPUs time line

Erik Lindahl erik.lindahl at gmail.com
Thu Jan 19 13:03:22 CET 2017

All changes are available in the sense that they are public, but there is no guarantee whatsoever that they produce correct results or are representative of the performance that will be in the release.

Not that we think it's bad, but the main reason things haven't been committed is that it's not completely ready yet. 

Feel free to play with them, but we want to spend the efforts on finishing the changes rather than supporting unfinished ones :-)



Erik Lindahl <erik.lindahl at scilifelab.se>
Professor of Biophysics
Science for Life Laboratory
Stockholm University & KTH
Office (SciLifeLab): +46 8 524 81567
Cell (Sweden): +46 73 4618050
Cell (US): +1 267 3078746

> On 19 Jan 2017, at 11:52, Jochen Hub <jhub at gwdg.de> wrote:
> Hi Berk,
> many thanks for the quick reply. We are btw targeting purely throughput.
> Is the development tree somewhere available, so we can get a rough feeling on the performace on our GPUs?
> Many thanks,
> Jochen
>> Am 19/01/2017 um 09:30 schrieb Berk Hess:
>> Hi,
>> A basic version of PME on CUDA GPUs will be shipped with the 2017
>> release. Most likely this will only be single GPU, possibly with the
>> option to run pair interactions on one GPU and PME on another. The
>> changes up in gerrit are all working, but not complete yet. Aleksei has
>> a development tree with a complete implementation. The main question is
>> how much performance optimization and feature completion we can do
>> before the 2017 release.
>> PME on GPU will allow you to buy a CPU+GPU cluster with cheaper CPUs if
>> you are targeting throughput. It is less clear what the best setup will
>> be for the highest ns/day, since PME requires a lot of different kernels
>> which results in higher overheads.
>> Cheers,
>> Berk
>>> On 01/19/2017 08:55 AM, Jochen Hub wrote:
>>> Hi developers,
>>> I noticed that Aleksei has uploaded a whole bunch of commits for
>>> implenting PME for GPUs. Since we about to buy a new cluster, I was
>>> wondering if there is a rough time line when PME/CUDA code goes into
>>> master and realease branches. If PME runs smoothly on GPUs, the
>>> hardware with the best price/performance ratio obviously changes.
>>> Also, are the commits in the branch "master (pme)" already suitable
>>> for some preliminary benchmarking?
>>> Many thanks,
>>> Jochen
> -- 
> ---------------------------------------------------
> Dr. Jochen Hub
> Computational Molecular Biophysics Group
> Institute for Microbiology and Genetics
> Georg-August-University of Göttingen
> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
> Phone: +49-551-39-14189
> http://cmb.bio.uni-goettingen.de/
> ---------------------------------------------------
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