Feeds

Petascale powerhouse cracks important HIV code

Cray's Blue Waters simulates 64 million atoms

Protecting against web application threats using SSL

The Blue Waters petascale computer at the University of Illinois' National Centre for Supercomputing Applications is being credited with cracking part of the code of HIV – and possibly helping point the way to new treatments.

Simulations carried out on Blue Waters allowed researchers to determine the precise structure of the HIV capsid – the protein shell protecting the virus, which is an important part of its ability to attack the human immune system.

A sample of 64 million atoms was analysed, and according to the researchers, that's what required the petaflop capability of the supercomputer. What scientists were looking for was a detailed atomic-level analysis of the 1,300 identical proteins that form a cone-like structure in the capsid. Previously, attempts to analyse the capsid couldn't capture the whole structure in one simulation.

Preparing the ground for the experiment, the researchers, led by Peijun Zhang of the University of Pittsburgh had first conducted various physical experiments including cryo-electron tomography to slice the proteins up and gain a broad understanding of their shape. They then used Blue Waters to conduct a simulation, run by University of Illinois physics professor Klaus Schulten and postdoctoral researcher Juan Perilla, called “molecular dynamic flexible fitting”.

Schulten says the capsid is “one of the biggest structures ever solved”, with further explanation in the video below.

Watch Video

Blue Waters was originally going to be constructed by IBM, but Big Blue withdrew in 2011, realising it couldn't put the machine together on budget. Cray picked up the build, assembling XE6 Opteron blade server nodes and XK6 CPU-GPU nodes, linked with Cray's Gemini XE interconnect.

The 237 XE cabinets house more than 22,000 compute nodes, while the 32 XK cabinets are home to 3,072 compute nodes. There's 26.4 PB of storage with an aggregate I/O of more than a terabit per second. ®

Choosing a cloud hosting partner with confidence

More from The Register

next story
Wanna keep your data for 1,000 YEARS? No? Hard luck, HDS wants you to anyway
Combine Blu-ray and M-DISC and you get this monster
Google+ GOING, GOING ... ? Newbie Gmailers no longer forced into mandatory ID slurp
Mountain View distances itself from lame 'network thingy'
US boffins demo 'twisted radio' mux
OAM takes wireless signals to 32 Gbps
Apple flops out 2FA for iCloud in bid to stop future nude selfie leaks
Millions of 4chan users howl with laughter as Cupertino slams stable door
Students playing with impressive racks? Yes, it's cluster comp time
The most comprehensive coverage the world has ever seen. Ever
Run little spreadsheet, run! IBM's Watson is coming to gobble you up
Big Blue's big super's big appetite for big data in big clouds for big analytics
Seagate's triple-headed Cerberus could SAVE the DISK WORLD
... and possibly bring us even more HAMR time. Yay!
prev story

Whitepapers

Secure remote control for conventional and virtual desktops
Balancing user privacy and privileged access, in accordance with compliance frameworks and legislation. Evaluating any potential remote control choice.
WIN a very cool portable ZX Spectrum
Win a one-off portable Spectrum built by legendary hardware hacker Ben Heck
Storage capacity and performance optimization at Mizuno USA
Mizuno USA turn to Tegile storage technology to solve both their SAN and backup issues.
High Performance for All
While HPC is not new, it has traditionally been seen as a specialist area – is it now geared up to meet more mainstream requirements?
The next step in data security
With recent increased privacy concerns and computers becoming more powerful, the chance of hackers being able to crack smaller-sized RSA keys increases.