Folding Forum

I've opened an issue on the OpenMM issue tracker: https://github.com/openmm/openmm/issues/2986

~ John Chodera // MSKCC

Happy New Year, all! We've just launched a short pair of projects that examine the retrospective performance on ~130 compounds assayed with the isoquinoline scaffold considered in Sprint 5 to help us better understand which assembly state (monmer vs dimer) and protonation state for the Mpro catalyti...

We've just released GPU (core22) projects 13430-7. These simulations are X-ray structures collected from the COVID Moonshot ( http://covid.ai/postera ) that will help us pick better starting structures for the COVID Moonshot weekly sprints ( https://foldingathome.org/2020/07/28/introducing-covid-moo...

Apologies for all the difficulties here! Our lead developer was working on resolving some weird behavior with the server code on aws3.foldingathome.org, and appears to have solved these issues on Dec 21. aws3 now has a deployed version of the new debug code with the fix. Please do let us know if you...

We recently finished Sprint 5 for the COVID Moonshot ( https://foldingathome.org/2020/11/09/covid-moonshot-sprint-5/ ), and have now rolled out projects 13438-13440 that test some modified protocols for the same Sprint 5 compounds. We're hoping we can find some other potent compounds hiding in this ...

@MFicek: We hear you, and we primarily use Folding@home to work on cancer! You can check out more of what we do here: http://choderalab.org Much of the lab has been pitching in on our COVID work to develop a new small molecule therapy with the COVID Moonshot ( http://postera.ai/covid ), but we shoul...

A lot of what we've been doing with Folding@home recently has been focused on understanding mechanisms underlying disease by studying conformational transitions in the presence and absence of cofactors or disease-relevant mutations, or predicting how new molecules might bind and inhibit disease targ...

Interesting! Thanks for the heads up here---we'll raise this issue internally.

~ John Chodera // MSKCC

We've been working on building Folding@home cores for the ARM architecture used in the new M1 chip! It may take a while before we can use the GPU, but I believe the gromacs core has already been released for some ARM platforms. The bigger issue is rebuilding the client, but we've been making headway...

Looks like you folks depleted all our GPU WUs! I'm astounded, to be frank.

I've added a bit more WUs to 13428-9 to firm up our statistics on COVID Moonshot Sprint 5 until we have Sprint 6 and new antibody simulations ready to go in a couple of days.

~ John Chodera // MSKCC

> And now the Radeon VII, Vega are getting them again... <400k PPD...

This was my fault! I spotted what I thought was a misconfiguration, yesterday, but accidentally created this mess. Sorry about that! It's been corrected now.

~ John Chodera // MSKCC

Thanks for the heads up, folks! I've just restricted 13429 to GPUSpecies<5 for AMD so that it won't be assigned to VEGA 64 cards anymore.

~ John Chodera // MSKCC

It's finally here! COVID Moonshot Sprint 5 --- projects 13428-9 --- are launching now! 13428 is the protein-ligand complexes for new compound designs, and restricted to wide GPUs 13429 is the ligand in solvent, and restricted to narrow GPUs Blog post with more information about the science coming so...

If you're able to provide more information about which PROJ, RUN, CLONE, GENs this occurs with and which GPU(s), as well as whether the core was running in OpenCL or CUDA mode, that would be super helpful in tracking down the offending kernel(s)!

~ John Chodera // MSKCC

We're looking into this! Last time we encountered this, there was a specific kernel call that was taking a bit too long to make the windows timeout. We might be able to easily fix this without requiring settings to be changed.

~ John Chodera // MSKCC