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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.
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<div class="">Tim<br class="">
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<div class="">On 4 Feb 2021, at 14:52, Scott Atchley <<a href="mailto:e.scott.atchley@gmail.com" class="">e.scott.atchley@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">On Thu, Feb 4, 2021 at 9:23 AM Jörg Saßmannshausen <<a href="mailto:sassy-work@sassy.formativ.net" class="">sassy-work@sassy.formativ.net</a>> wrote:<br class="">
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One of the things I heard a few times is the use of GPUs for the analysis. Is <br class="">
that something you are doing as well? </blockquote>
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<div class="">ORNL definitely is. We were the first to contribute cycles to the COVID-19 HPC Consortium:</div>
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<div class=""><a href="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=" class="">https://www.olcf.ornl.gov/2020/03/30/summit-joins-the-covid-19-high-performance-computing-consortium/
[olcf.ornl.gov]</a><br class="">
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<div class="">Two finalists for the SC19 Gordon Bell special prize on COVID research used Summit:</div>
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<div class=""><a href="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=" class="">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]</a><br class="">
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<div class="">One of which won the prize:</div>
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<div class=""><a href="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=" class="">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]</a><br class="">
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Also, on the topic of GPUs (and being a <br class="">
bit controversial): are there actually any programs out there which are not <br class="">
using nVidia GPUs and use the AMD ones for example?</blockquote>
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<div class="">LLNL is with their Corona system:</div>
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<div class=""><a href="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=" class="">https://www.llnl.gov/news/upgrades-llnl-supercomputer-amd-penguin-computing-aid-covid-19-research
[llnl.gov]</a> </div>
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