Feeds

Petascale powerhouse cracks important HIV code

Cray's Blue Waters simulates 64 million atoms

5 things you didn’t know about cloud backup

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. ®

Build a business case: developing custom apps

More from The Register

next story
Microsoft: Azure isn't ready for biz-critical apps … yet
Microsoft will move its own IT to the cloud to avoid $200m server bill
Shoot-em-up: Sony Online Entertainment hit by 'large scale DDoS attack'
Games disrupted as firm struggles to control network
Silicon Valley jolted by magnitude 6.1 quake – its biggest in 25 years
Did the earth move for you at VMworld – oh, OK. It just did. A lot
VMware's high-wire balancing act: EVO might drag us ALL down
Get it right, EMC, or there'll be STORAGE CIVIL WAR. Mark my words
Forrester says it's time to give up on physical storage arrays
The physical/virtual storage tipping point may just have arrived
VMware vaporises vCHS hybrid cloud service
AnD yEt mOre cRazy cAps to dEal wIth
prev story

Whitepapers

A new approach to endpoint data protection
What is the best way to ensure comprehensive visibility, management, and control of information on both company-owned and employee-owned devices?
Implementing global e-invoicing with guaranteed legal certainty
Explaining the role local tax compliance plays in successful supply chain management and e-business and how leading global brands are addressing this.
Maximize storage efficiency across the enterprise
The HP StoreOnce backup solution offers highly flexible, centrally managed, and highly efficient data protection for any enterprise.
How modern custom applications can spur business growth
Learn how to create, deploy and manage custom applications without consuming or expanding the need for scarce, expensive IT resources.
Next gen security for virtualised datacentres
Legacy security solutions are inefficient due to the architectural differences between physical and virtual environments.