I'm making some strong decisions here and if they offend you they offend
you but I'm the one doing the work here and that gives me the ability to do
exactly that. I've already accepted that whatever I'm building won't be
called pmemd because I'm going to FOSS it and ride the AI in drug Discovery
wave AlphaFold 2 triggered. It would have been nice, but it's not a
deal-breaker. Nothing to see here, move along.
On Mon, Aug 8, 2022, 08:18 Adrian Roitberg via AMBER-Developers <
amber-developers.ambermd.org> wrote:
> Didi you actually meant to send this to the WHOLE dev list ?
>
> nice move.
>
>
> On 8/5/22 3:36 PM, Scott Le Grand via AMBER-Developers wrote:
> > [External Email]
> >
> > Private profanity-laden personal email attacks and insinuations about my
> > motives aside Adrian (and I won't post them here because shame on you
> but I
> > am petty enough to mention it because transparency is everything and what
> > you wrote ought to be beneath you), spending 8+ months in this code has
> led
> > to strong opinions about what happened to it and what ought to be done
> > about it. I'm happy to discuss those opinions with anyone who's willing
> to
> > invest anywhere close to that much effort reviewing the codebase and I'd
> > love a genuine collaborator here, but it doesn't seem like anyone has my
> > level of interest in refactoring PMEMD out of its situation (Cerutti's
> > gone, and Taisung seems like he wants to science and that's OK), and I've
> > already accepted that whatever I build won't be called PMEMD because I am
> > going 100% FOSS with it and PMEMD isn't, but it will be a successor to
> it.
> >
> > But that ought not to be controversial IMO, but alas, everything's
> > controversial these days, no? NEB was a clear cut case for a braindead
> > simple GPU kernel anyone with a modicum of interest in CUDA could write
> and
> > there are plenty of examples in the code already for AMD, GAMD, the
> Scalar
> > Sum, the update and EField on which to base it. Its addition to PMEMD
> > should have been blocked until the author spent the time on it IMO. Water
> > under the bridge now, but yeah, shuttle is dead dead dead. And if anyone
> > ends up using what I built, they can build GPU NEB in a day with the API
> > even in its primordial state. And they can even do it on the CPU, but it
> > won't be in the codebase, it will be in the model zoo where it belongs
> > along with most of the other drive-by additions to PMEMD. And that ought
> to
> > ameiiorate the bitrot. Or not, we'll see.
> >
> > But hybridizing a GPU codebase with the CPU is everything wrong with
> > GROMACS. It works fantastically when both the CPU and the GPU are SOTA
> but
> > results are not typical. The reason I went 100% GPU was so that even a
> > craptastic ARM chip in an embedded system would deliver 95+% the GPU
> > performance of a SOTA CPU driving that GPU so as to enable post-docs and
> > grad students to upgrade their GPUs independently of their workstations
> to
> > accelerate their research without breaking the bank as well as cut down
> on
> > e-Waste. Plus GPUs are moving exponentially faster than CPUs so CPUs
> > inevitable become decelerators or e-Waste. Whatever else you think of me,
> > that's my story and I have 20+ patents and 6-figures of lines of code out
> > there to back it up.
> >
> > But by all means dismiss my entire career. Dismissing expertise and
> wisdom
> > is really the rage now. Yikes.
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> >
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber-developers&data=05%7C01%7Croitberg%40ufl.edu%7C689b3a8529e244b1a73308da7719e7ca%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C637953250384373192%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pHNFjSzPLUZdie6sMp%2BLDojN5ntO2fojRfsg%2FqtebU4%3D&reserved=0
>
> --
> Dr. Adrian E. Roitberg (he/him/el)
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Mon Aug 08 2022 - 08:30:03 PDT
