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Comment: Re:Really bad explanation of the evolution. (Score 1) 133

by dmbasso (#47375287) Attached to: Tibetans Inherited High-Altitude Gene From Ancient Human

Because you said that thousands of years ago specific genes were transplanted

No, I didn't say that. The example I gave was only to elucidate that a single gene (or even a bunch of them) doesn't define a population. I read my post again and the message still seems clear. But ok, I'll make it fucking transparent: suppose I write a book and copy an entire paragraph of Shakespeare's Hamlet, then proceed to burn every single copy of the aforementioned play. It doesn't matter that a paragraph continues to exist in another book, Hamlet went extinct.

Comment: Re:Really bad explanation of the evolution. (Score 1) 133

by dmbasso (#47374811) Attached to: Tibetans Inherited High-Altitude Gene From Ancient Human

I haven't said Denisovans were a different species... you are aware that the word "extinction" is not limited to species right? If all Caucasians | Africans | Mongolians died, their population would be extinct. Their genes would still survive in other humans, and that doesn't make any difference to the fact they would be extinct.

And how the fuck did you read religious connotations in my post? I'm an atheist.

Comment: Re:Really bad explanation of the evolution. (Score 2) 133

by dmbasso (#47374119) Attached to: Tibetans Inherited High-Altitude Gene From Ancient Human

The explanation of the evolution is terrible. If the gene was inherited from a "Denisovans" then that Denisovan didn't go extinct. His descendents are still among us. The gene did not spread through the population; the people who had the gene survived and people without the gene disappeared leaving more space for those survivors.

Yes, the "people with the gene" were called Denisovans, they "disappeared", therefore they did go extinct. It seems you don't follow the logic of your own statements.

And just to make it even more clear: suppose I make dog with the tomato gene for photosynthesis (a solar powered dog, how cool is that), then kill every single tomato plant in the world with some Monsanto shit. It doesn't matter that my glorious green power efficient dog would carry the tomato gene... tomatos would still have gone extinct.

Comment: Yesno? (Score 1) 89

by gentryx (#47300321) Attached to: Computing a Cure For HIV

It's not that specialized. It's just plenty of DSPs strapped together on a torus.

Actually Anton uses ASICS, their cores are specially geared at MD codes. This goes way beyond just "strapping together DSPs". They have IIRC ~70 hardware engineers on site. (Source: I've been to DE Shaw Research last year).

Unlike what wikipedia claims, you could probably achieve comparable performance using a more classical and general-purpose supercomputer setup with GPU or Xeon Phi accelerators, provided the network topology is well tuned to address this sort of communication scheme

No, you can't, and here is why: Anton is built for strong scaling of smallish, long running simulations. If you ran the same simulations on a "x86 + accelerator" system (think ORNL's Titan) then you'd observe two effects:

  • The GPU itself might idle a lot as each timestep only involves few computations, leaving many shaders idle or waiting for the DRAM.
  • Anton's network is insanely efficient for this use case. IIRC it's got a mechanism equivalent to Active Messages, so when data arrives, the CPU can immediately forward it to the computation which is waiting for it. That leads to a very low latency compared to a mainstream "InfiniBand + GPU" setup.

(most recent supercomputers don't use tori)

Let's take a look at the current Top 500:

  • #1 Tianhe-2: Fat Tree
  • #2 Titan: 3D Torus
  • #3 Sequoia: 5D Torus
  • #4 K Computer: 6D Torus
  • #5 Mira: 5D Torus
  • #6 Piz Daint: 3D Torus
  • #7 Stampede: Fat Tree
  • #8 JUQUEEN: 5D Torus
  • #9 Vulcan: 5D Torus
  • #10 nn: 3D Torus

So, torus networks are the predominant topology for current supercomputers.

Comment: Missing: Project Pluto (Score 3, Interesting) 133

by gentryx (#47294363) Attached to: The Revolutionary American Weapons of War That Never Happened
Granted, it sounds a tad like an episode from Thunderbirds, but it's real: Project Pluto was a nuclear powered Supersonic Low Altitude Missile (SLAM). The idea was to drive the reactor into critical state and superheat the inflowing air, efficiently creating a nuclear powered scamjet. Downside: because the reactor was almost unshielded, all controls had to be designed to withstand extreme radiation and heat (they had to work in white heat conditions). The project was canceled in the 60s, but they actually built and powered up the engines.

Comment: /Very/ different hardware (Score 2) 89

by gentryx (#47290013) Attached to: Computing a Cure For HIV

Computational drug design and bitcoin miners have in common that both run best on custom hardware. The crux is, that both require very different types of hardware. As an example, please refer to Anton, designed by DE Shaw Research exactly for molecular dynamics (MD) codes.

Bitcoin mining is classified as a so called embarrassingly parallel algorithm, while MD is a tightly coupled problem. Hence an efficient parallelization for MD codes is much harder to speed up: communication gets in the way, and communication is essentially always bound by the speed of light.

ps: fun fact: bitcoin mining and MD can be carried out (at least somewhat) efficiently on GPUs.

Comment: Re:what? (Score 1) 80

by dmbasso (#47276163) Attached to: Intel To Offer Custom Xeons With Embedded FPGAs For the Data Center

I would assume the FPGA part of the CPU would be programmed in VHDL.

Yes, that's the obvious reasoning. And that's certainly interesting enough on its own. But the summary said

[...]for critical functions without translating the majority of their code[...]

Somebody has to do the translation, agree?

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