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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.

+ - George R R Martin Reveals His Secret Weapon for Writing GOT- Wordstar

Submitted by Hugh Pickens DOT Com
Hugh Pickens DOT Com (2995471) writes "Ryan Reed writes that when most Game of Thrones fans imagine George R.R. Martin writing his epic fantasy novels, they probably picture the author working on a futuristic desktop (or possibly carving his words onto massive stones like the Ten Commandments). But the truth is that Martin works on an outdated DOS machine using Eighties word processor WordStar 4.0, as he revealed during an interview on Conan. "I actually like it," says Martin. "It does everything I want a word processing program to do, and it doesn't do anything else. I don't want any help. I hate some of these modern systems where you type a lower case letter and it becomes a capital letter. I don't want a capital. If I wanted a capital, I would have typed a capital. I know how to work the shift key." “I actually have two computers," Martin continued. “I have a computer I browse the Internet with and I get my email on, and I do my taxes on. And then I have my writing computer, which is a DOS machine, not connected to the Internet.""

Comment: Catching the stolen bitcoins... (Score 1) 695

by gentryx (#46334623) Attached to: Mt. Gox Gone? Apparent Theft Shakes Bitcoin World
The list of robbed Bitcoin exchanges is long and growing. In almost all cases the stolen coin can be traced (since all transactions are public thanks to the protocol). I wonder if the running exchanges have some sort of blacklist that detects whether previously stolen funds get moved to their wallets and if they will confiscate those.

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