Thanks for the update. My own supercomputer experience is nearly 20 years out of date. I demoed our MD work in the HP booth back in SC'94, and IBM for SC '95. Even then it was apparent that MD required good interconnect to match the increases in CPU.

Beyond that though, I don't know where this conversation should go. I could be cynical and point out that the proposals you all accepted, while worthy, look similar to the proposals from 20 years ago but with "SP-2" or "cluster" scratched out and replaced with "Exacycle." Even some of the names (Russ Altman, GROMOS/GROMACS) have little changed in the last 15 years.

I could observe, as you did in passing, that this project does not turn "1-10 year projects" into "an overnight job" because writing the software and understanding the results dominates the overall time - otherwise they would be done, no? And realistically, few people embark on 10 year projects; they estimate 10 years then work on another project which is more tractable, with the hope that in 10 years it will become a 2 year project.

I could go the Greg Wilson route, and argue that the "Real Bottleneck in Scientific Computing" is not the CPU cycles but the need for better training in computational scientists in how to write and organize software, and a cultural change in how journals treat software development and testing. Yet supercomputers gets a large amount of funding compared to training.

Or I could quizzically wonder why it is that "interesting", "theoretical" work isn't exactly the sort of work that researchers should be doing. For example, "InChIKey collision resistance: an experimental testing", doi:10.1186/1758-2946-4-39 shows that related work is easily publishable.

And I further wonder how my conversations with people at pharmas, about how they might use the InChIKey, is "complicated." It was someone at AstraZeneca who told me they were evaluating the use of InChI keys in order to link internal databases to external web search engines and data sets without triggering the usual reactions against revealing internal structure information. They thought to generate the hash for each compound, make a hyperlink to the external site using that hash, and they are done. That seemed reasonable to me then. Over time I've wondered just how safe it actually is. Can pharmas actually use InChI keys to do things that they can't do with "existing IP protection mechanisms"? Are they leaking data already, without realizing it? If so, what is the level of leakage?

But realistically, or perhaps back to cynically, justifications like "could cure cancer" or the newer "could help identify new antibiotics", or like "help understand disease" or "reveal insights into fundamental biochemistry" are ever so much easier to justify funding than the mundane "train computational chemists in how to program" or "see if there are new ways to exchange proprietary data between distrusting organizations".

What, me bitter? Perhaps slightly, but I've decided that there's much more interesting diversity in the sorts of problems that one person or a small group can work on, without having to justify its practicality or how it fits into some long-term Grand Challenge vision. It just means that there are some interesting projects which need high-end compute power that I just can't work on. Yet.