Indeed. We’re actively looking at these as well. GPUs can be used for a lot
of this stuff (e.g. the Parabricks product on nVidia GPUs) and they’re an
inherent part of some sequencers. The base called on the Oxford Nanopore
system is an ML algorithm, and ONT worked with nVidia on that, I believe.
Tim
On 4 Feb 2021, at 14:52, Scott Atchley
<[email protected]<mailto:[email protected]>> wrote:
On Thu, Feb 4, 2021 at 9:23 AM Jörg Saßmannshausen
<[email protected]<mailto:[email protected]>> wrote:
One of the things I heard a few times is the use of GPUs for the analysis. Is
that something you are doing as well?
ORNL definitely is. We were the first to contribute cycles to the COVID-19 HPC
Consortium:
https://www.olcf.ornl.gov/2020/03/30/summit-joins-the-covid-19-high-performance-computing-consortium/
[olcf.ornl.gov]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.olcf.ornl.gov_2020_03_30_summit-2Djoins-2Dthe-2Dcovid-2D19-2Dhigh-2Dperformance-2Dcomputing-2Dconsortium_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=gSesY1AbeTURZwExR_OGFZlp9YUzrLWyYpGmwAw4Q50&m=t0E7cT3unqmX-z0puDoX5kfCvxwH2UGcZ23fM8ivaUA&s=0IPvce9v3A1kjMuq_as3E8k3xrn2yva4g9Ch2GhFCoE&e=>
Two finalists for the SC19 Gordon Bell special prize on COVID research used
Summit:
https://www.olcf.ornl.gov/2020/11/18/two-finalists-nominated-for-gordon-bell-special-prize-for-covid-19-work-on-summit/
[olcf.ornl.gov]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.olcf.ornl.gov_2020_11_18_two-2Dfinalists-2Dnominated-2Dfor-2Dgordon-2Dbell-2Dspecial-2Dprize-2Dfor-2Dcovid-2D19-2Dwork-2Don-2Dsummit_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=gSesY1AbeTURZwExR_OGFZlp9YUzrLWyYpGmwAw4Q50&m=t0E7cT3unqmX-z0puDoX5kfCvxwH2UGcZ23fM8ivaUA&s=urvj498utX3JdAevLBR6HwCWHYouon4QB_H9GOC4v4I&e=>
One of which won the prize:
https://www.olcf.ornl.gov/2020/11/18/multi-institutional-team-earns-gordon-bell-special-prize-finalist-nomination-for-rapid-covid-19-molecular-docking-simulations/
[olcf.ornl.gov]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.olcf.ornl.gov_2020_11_18_multi-2Dinstitutional-2Dteam-2Dearns-2Dgordon-2Dbell-2Dspecial-2Dprize-2Dfinalist-2Dnomination-2Dfor-2Drapid-2Dcovid-2D19-2Dmolecular-2Ddocking-2Dsimulations_&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=gSesY1AbeTURZwExR_OGFZlp9YUzrLWyYpGmwAw4Q50&m=t0E7cT3unqmX-z0puDoX5kfCvxwH2UGcZ23fM8ivaUA&s=MtHGgLo1Hss1qDAj7Fv1ZSjmUDtkPBj5yukIBjgyZgA&e=>
Also, on the topic of GPUs (and being a
bit controversial): are there actually any programs out there which are not
using nVidia GPUs and use the AMD ones for example?
LLNL is with their Corona system:
https://www.llnl.gov/news/upgrades-llnl-supercomputer-amd-penguin-computing-aid-covid-19-research
[llnl.gov]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.llnl.gov_news_upgrades-2Dllnl-2Dsupercomputer-2Damd-2Dpenguin-2Dcomputing-2Daid-2Dcovid-2D19-2Dresearch&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=gSesY1AbeTURZwExR_OGFZlp9YUzrLWyYpGmwAw4Q50&m=t0E7cT3unqmX-z0puDoX5kfCvxwH2UGcZ23fM8ivaUA&s=OPKyBmhreQGgZoeZDKw4oo2g-qFAkk9NOBhFx6BdTqk&e=>
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