The Leading Source for Global News and Information Covering the Ecosystem of High Productivity Computing
December 14, 2007
DEISA, GridAustralia Demo HIV Drug Simulations Over Grid
Dec. 12 -- DEISA, the Distributed European Infrastructure for Supercomputing Applications, and GridAustralia-APAC, joined by Monash University, have demonstrated interoperation of their HPC infrastructures with distributed simulations in both continents on the effectiveness of drugs on mutants of the Human Immunodeficiency Virus (HIV).
The AIDS disease effects over 40 million people worldwide. Certain drugs have the ability to reduce patient viral loads and improve patient health by binding to and inhibiting critical viral enzymes. Unfortunately, the HIV virus causing AIDS has the ability to mutate and become resistant to these drugs. That sometimes happens in a very short period of time, thus requiring the patients to change their drug regime. As new mutations arise, it is important to pick the right anti-viral drug to best treat the patient and to not encourage the development of further drug resistance.
According to Michael Kuiper from VPAC, simulations have been designed to gather drug binding interaction energies of anti-HIV drugs bound to the active site of HIV protease, including drug-resistant versions of the protein. Though a methodology with still ongoing development, it is hoped that this technique can give an accurate assessment of the likely effectiveness of each antiviral drug with respect to any given HIV mutant strain.
Given this information, patients who develop drug resistance can be given the next best effective drug for their HIV strain while reducing the danger of further resistance enhancements. In order to assess the drug binding interactions, each drug and respective HIV mutant enzyme is run as a short molecular dynamics simulation to try and get an averaged energy of interaction between the drug and the HIV protease strain. The huge number of calculations required is well suited for distributed processing, and time-to-solution can be significantly reduced by employing at the same time several supercomputers in a suitable HPC grid. Given a certain level of interoperability, the compute tasks can even be spread over different grids.
This effort has been successfully undertaken by DEISA and GridAustralia-APAC, joined by Monash University, during SC07 in Reno, although both infrastructures use different, incompatible underlying main middleware platforms.
DEISA is based on UNICORE 5 as far as job submission is concerned, while APAC makes use of the Globus Tool Kit. Following different approaches in job management, Globus and UNICORE are not interoperable in their currently established versions. In addition to DEISA's option of data management via a continental global file system, however, both infrastructures support data transfer via GridFTP, usable both in Globus and in UNICORE.
Input data sets were provided in Australia by the Australian Research Group on an APAC storage server. Series of workflow jobs were submitted as shell scripts at the client site both to DEISA and to APAC through infrastructure specific interfaces, using DESHL for DEISA (a UNICORE command line tool), and Globus WS-Gram client for APAC. The parts of the input data required by each job were automatically moved to the respective DEISA or APAC execution sites in Europe or Australia via GridFTP.
A number of simulations were run with the drug Amprenavir (Apv) acting on various HIV strains. The trajectory data was post-processed to measure the energy of interaction between the drug and each HIV strain. The simulation results were later automatically uploaded on that APAC storage server for post-processing and visualization by the researchers.
By this transparent linking of compute resources in Australia and in Europe, and by offering reliable, automated bidirectional data transfer between both infrastructures, this project-oriented interoperation of DEISA and APAC could successfully be demonstrated for the first time.
-----
Source: DEISA
Article Tools
Share Options
(Digg, Technorati, more)
Subscribe
Sponsored Links
RSS Feeds
Feeds by Topic
- Applications
- Developer Tools
- Interconnects
- Middleware
- Networks
- Processors
- Storage
- Systems
- Visualization
Feeds by Industry
Feeds by Content Type
Feature Articles
TeraGrid '09: Student Participation Soars
There was a new energy at this year's TeraGrid '09 conference thanks to an outstanding turnout for the student program. Thanks to support from the National Science Foundation, more than 100 high school, undergraduate and graduate students were able to participate in the conference.
Read More...
TeraGrid '09: OSG and TeraGrid Collaboration
Paul Avery, a recognized leader in advanced grid and networking for science, delivered the first keynote address at the recent TeraGrid '09 conference in Arlington, Virginia. A professor of physics at the University of Florida, Avery is co-principal investigator and founding member of the Open Science Grid (OSG). Avery talked about the history of OSG, some of the projects that leverage its resources, and OSG's relationship with TeraGrid.
Read More...
TeraGrid '09: Thriving in an Exponentially Changing World
Before he even took the podium, Ed Seidel was one of the buzz makers at the TeraGrid '09 conference. The day before his keynote, it was announced that he was stepping in as acting assistant director of the National Science Foundation's math and physical sciences directorate. For his talk at the conference, however, Seidel focused on the issues and efforts within his home at NSF, the Office of Cyberinfrastructure.
Read More...
Top Headlines
3D Seismic Data: Taking a Smarter Approach to Interpretation
Jul 09 | Engineer Live | The demand for computational tools to underpin the 3D seismic interpretation process has never been more apparent. Read more...
Engineering Unemployment Soared in 2Q to 8.6%
Jul 08 | EE Times | Unemployment for U.S. engineers has reached record levels, according to government figures. Read more...
Gartner Adjusts 2009 IT Spend Downward Again
Jul 08 | Network World | Global spending for 2009 projected to drop 6 percent, for a total of $3.2 trillion. Read more...
Concurrent and Parallel Are Not The Same
Jul 08 | Linux Magazine | Portability or efficiency? Neither is guaranteed when writing explicit parallel code. Read more...
800 TFLOP Real-Time Ray Tracing GPU Unveiled, Not for Gamers
Jul 07 | Ars Technica | Japanese company builds custom ASIC to accelerate real-time ray traced rendering for the auto industry. Read more...
Featured Whitepapers
Building High Performance Computing in a Green and Modular Solution Building Block
Apr 14 | | Many HPC IT departments are feeling the rising pressure to deliver more capacity computing and performance while trying to reduce the total cost of ownership. This white paper discusses how an environmentally-friendly and open-standards HPC building block based computing system using flexible interconnect options helps address capacity computing needs.
Multimedia
Webcast: Dell Expands HPC Access and Adoption with Intel Cluster Ready Program
Source: Addison Snell, GM/VP, Tabor Research; sponsored by Dell
Many organizations that could benefit from the use of HPC clusters find that it is complicated to get the systems up and running because of limited IT resources or the complexities of the clusters themselves. Learn how the Intel Cluster Ready program, for which Dell was an original partner, seeks to address this challenge for entry level and mid-range HPC users.
Video White Paper: Architecting a Better Network Storage Solution
BlueArc's Titan architecture represents an evolutionary step in file servers by creating a hardware-based file system that can scale bandwidth, IOPS, and overall data capacity well beyond conventional software-based devices. With its ability to virtualize a massive storage pool of up to four usable petabytes of tiered storage, Titan can scale with growing data requirements, offering a competitive advantage for businesses, researchers, or other enterprises seeking to better manage data growth while still ensuring optimal performance.
Webcast: HPC Development Solutions: Sun Studio & Sun HPC ClusterTools
Sun Studio Compilers and Tools and Sun HPC ClusterTools allow you to create high performance parallel applications for OpenSolaris, Solaris and Linux. Sun Studio Express 11/08 includes MPI performance analysis capabilities and full OpenMP 3.0 compiler support. Learn about all this and the latest in Sun HPC ClusterTools 8.1.
Newsletters
Stay informed! Subscribe to HPCwire email Newsletters.
HPC Job Bank
-
HPC Systems Administrator
McGill University -
High Performance Computing Data Center Manager
National Renewable Energy Laboratory -
High Performance Computing Systems Administrator
Idaho National Laboratory -
Solution Engineer- HPC
Dell Inc -
Parallel Programmer
Cardiff University -
Principal Software Research Engineer
Indiana University -
Post Doctoral Researcher - Exascale Stream Computing
IBM - Visit the HPCwire Job Bank
Featured Events
-
July 13-16, 2009
WORLDCOMP'09
Las Vegas , NV
USA
-
August 24-28, 2009
Data Mining: Levels I, II, & III
Denver , CO
USA