Feeds

Petascale powerhouse cracks important HIV code

Cray's Blue Waters simulates 64 million atoms

Beginner's guide to SSL certificates

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. ®

Security for virtualized datacentres

More from The Register

next story
It's Big, it's Blue... it's simply FABLESS! IBM's chip-free future
Or why the reversal of globalisation ain't gonna 'appen
'Hmm, why CAN'T I run a water pipe through that rack of media servers?'
Leaving Las Vegas for Armenia kludging and Dubai dune bashing
Facebook slurps 'paste sites' for STOLEN passwords, sprinkles on hash and salt
Zuck's ad empire DOESN'T see details in plain text. Phew!
CAGE MATCH: Microsoft, Dell open co-located bit barns in Oz
Whole new species of XaaS spawning in the antipodes
Microsoft and Dell’s cloud in a box: Instant Azure for the data centre
A less painful way to run Microsoft’s private cloud
AWS pulls desktop-as-a-service from the PC
Support for PCoIP protocol means zero clients can run cloudy desktops
prev story

Whitepapers

Choosing cloud Backup services
Demystify how you can address your data protection needs in your small- to medium-sized business and select the best online backup service to meet your needs.
Forging a new future with identity relationship management
Learn about ForgeRock's next generation IRM platform and how it is designed to empower CEOS's and enterprises to engage with consumers.
Security for virtualized datacentres
Legacy security solutions are inefficient due to the architectural differences between physical and virtual environments.
Reg Reader Research: SaaS based Email and Office Productivity Tools
Read this Reg reader report which provides advice and guidance for SMBs towards the use of SaaS based email and Office productivity tools.
Storage capacity and performance optimization at Mizuno USA
Mizuno USA turn to Tegile storage technology to solve both their SAN and backup issues.