NCSA's first Itanium Linux cluster shows top performance in test runsChampaign 18 October 2001 The world's largest Linux cluster running on Intel's 64-bit Itanium architecture has been put through its first full-scale operational test, and results show the system to be extremely scalable and faster than more traditional high-performance computing systems.
The cluster, named Titan, consists of 160 dual-processor IBM IntelliStation machines based on the Itanium architecture. Titan was installed at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign in August. It will be available for use by the academic research community later this year.
Currently NCSA technical staff are conducting test runs on the cluster as part of their effort to determine its performance capabilities and ready it for general scientific use. A recent run using the NAMD molecular dynamics code proved that the cluster scales extremely well up to 300 processors and that it can dramatically decrease the time needed to compute complicated molecular dynamics simulations. In the test runs, Titan broke the one-day barrier for computing one nanosecond of simulation time using NAMD. The runs used 256 processors, and the results were more than two times faster than the previous best results.
The run marked the first time that NAMD was able to compute as much as one nanosecond of a benchmark simulation per day. The NAMD code was created by University of Illinois physicist Klaus Schulten and his research team in the Beckman Institute's Theoretical Biophysics Group, a research and development center funded by the National Institutes of Health. Biomolecular simulations look at processes in living cells at an atomic scale. They provide a look at the cell's molecular machinery, which consists of hundreds of thousands of atoms.
Simulations on this scale require massive computing power, and it can often take days or weeks to simulate one nanosecond of biomolecular activity. Runs done by Schulten's group last summer used 135,000 CPU hours on NCSA's Pentium III Linux cluster and simulated activity in 327,000 atoms over 3.8 nanoseconds.
These complex simulations also depend on computer systems that can scale up and utilise hundreds of processors at a time. The NAMD runs done last summer, for example, would have taken 15 years on a single processor.
"From my perspective, it is important to alert the community of biomolecular modelers to the fact that Itanium Linux clusters work so well for molecular dynamics simulations, and that they will allow a research team to look at larger problems and do new science", said Mr. Schulten. "If NAMD can achieve such performance, other modelling programmes should be able to do it too. Having these Linux clusters available to researchers will be a great resource for modellers all around the country."
Both Titan and the Pentium III Linux cluster named Platinum have a peak performance of 1 teraflops, or a trillion calculations per second. The two clusters are NCSA's first terascale computers and will become part of the TeraGrid computing system. NCSA is working with three academic and several corporate partners to create the TeraGrid, the world's largest, fastest, most comprehensive, distributed infrastructure for open scientific research. When completed, the TeraGrid will include 13.6 teraflops of Linux cluster computing power distributed at sites in Illinois and California.
For more on NAMD, visit http://www.ks.uiuc.edu/Research/namd/
For more on the Theoretical Biophysics Group, visit http://www.ks.uiuc.edu/.
Ad Emmen |
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