[Beowulf] Project Heron at the Sanger Institute [EXT]

[Tim Cutts]

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 <e.scott.atchley at gmail.com<mailto:e.scott.atchley at gmail.com>> wrote:

On Thu, Feb 4, 2021 at 9:23 AM Jörg Saßmannshausen <sassy-work at sassy.formativ.net<mailto:sassy-work at sassy.formativ.net>> 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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