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By Mike Gannis

Philip Papadopoulos

Greg Bruno,
Mason Katz,
Bill Link,
David McIntosh, Federico Sacerdoti

Philip Buonodanna, Bret Chun,
David Culler,
Eric Fraser,
Albert Goto,
Matt Massie

Millennium Group,
UC Berkeley
Laurence Liew,
Najib Ninaba
Linux Competency

Centre in SCS Enterprise Systems Pte. Ltd., Singapore
Putchong Uthayopas

The Open Scalable Cluster Environment, Thailand

Researchers with the National Partnership for Advanced Computational Infrastructure (NPACI) at the San Diego Supercomputer Center (SDSC) marked significant milestones this spring for the NPACI Rocks toolkit, which enables colleges, universities, research institutes, and other organizations to easily set up and manage powerful yet inexpensive cluster computers. As of June 26, the peak processing speed of 110 cluster computers administered by users of the NPACI Rocks software suite exceeded 17.6 teraflops (trillion floating point operations per second). In June 2003, four clusters administered with NPACI Rocks–at Dell Computer Corp., Hong Kong Baptist University, Stanford University, and Scripps Institution of Oceanography–were included in the Top500 list of the world's most powerful supercomputers. Researchers around the world are using that computing power to develop new nanomaterials, model population dynamics, predict urban water supplies, and perform many other research and education functions.

"The aggregate power of the clusters running NPACI Rocks is in the same league as the largest supercomputer systems in the world," said Philip Papadopoulos, program director for SDSC’s Grid and Cluster Computing group. "The number of systems and processors demonstrates the acceptance of NPACI Rocks in the user community."

Commodity clusters based on PC-type processors (Beowulf clusters) provide impressive power, considering their low cost. However, managing the clusters–ensuring that all of the nodes have a consistent set of software when patches and new versions of the operating system, utilities, and tools are released–can burden system administrators. Unfortunately, the costs of not managing a cluster can be even more expensive if security holes and known bugs in the system software are not patched.

"SDSC’s Cluster Group and UC Berkeley’s Millennium group began to work together on the NPACI clusters project three years ago," Papadopoulos said. "Our constant goal has been to make clusters easy to deploy, manage, upgrade, and scale."

The following summaries illustrate the variety of ways in which clusters built with NPACI Rocks are advancing scientific research:

Stanford University

The Bio-X Project is Stanford’s set of university-wide collaborations in basic, applied, and clinical sciences. The program brings together engineering, physics, chemistry, and the information sciences with biology and medicine to foster discoveries and inventions. The Schools of Engineering, Medicine, Humanities and Sciences, and Earth Sciences teamed up to form the new program.

The project has deployed a Pentium 4 cluster called Iceberg with 302 dual-processor nodes; it runs at more than 3.3 teraflops.

"When I evaluated NPACI Rocks, it seemed to answer all my questions and delivered the solution that met everyone’s needs," said Bio-X system administrator Steve Jones. "I can attest to the ease of management by using the Rocks distribution. We now are considering our next cluster; at this point, we think we will go with a 600-node dual-processor system, twice the size of our existing one. Given the successes that we’ve had so far, NPACI Rocks will of course be what we use to manage the next evolution of Iceberg."

Singapore Computer Systems

The Linux Competency Centre at Singapore Computer Systems (SCS-LCC) has set up a new 60-processor Itanium 2 cluster for the Singapore-MIT Alliance (SMA) at the National University of Singapore, its third cluster running NPACI Rocks. The new "Hydra III" cluster supports projects ranging from computational fluid dynamics to bio-engineering. About 50 SMA researchers and post-graduate students use the system. The cluster consists of 15 HP rx5670 nodes, each with four Itanium 2 processors, and is interconnected with a high-performance, high-bandwidth, low-latency switching system from Myrinet. Hydra III achieves 240 gigaflops, which is about 70 percent of theoretical peak processing power.

"The team took less than a day to install the cluster with Rocks and get the cluster operational," said Laurence Liew, a principal investigator at SCS. "This is a testimony to the amount of work that has gone into making Rocks one of the best and easiest to use cluster toolkits in the world."

"SCS Linux Competency Centre collaborates closely with SDSC on NPACI Rocks and provides critical support in the areas of file systems and queuing systems," said SDSC’s Papadopoulos. "The Rocks user community benefits greatly from SCS’s expertise and its significant contributions to this community toolkit."

"We are very pleased with the performance and ease of management of the Rocks-based Itanium 2 cluster," said Khoo Boo Cheong, a professor and program co-chair of High Performance Computation for Engineered Systems at SMA. "We intend to encourage more researchers to migrate to Hydra III over the next few months."

Scripps Institution of Oceanography,
UC San Diego

The Digital Image Analysis Lab’s PIPE (Parallel Image Processing Environment) cluster supports a wide variety of Earth systems science studies and applications, including those involving Earth-observing satellite data analysis, NASA’s Direct Broadcast program, snow hydrology and accurate water supply prediction, climate studies (especially related to the cryosphere), sea ice, airborne volcanic ash detection, agricultural applications, and basic and applied atmospheric and remote sensing sciences. The cluster supports a variety of disciplines in addition to Earth sciences–mathematics, computer science, spatial statistics, signal analysis, and electrical engineering, neural network analysis and other classification methods.

PIPE will be upgraded from 74 Pentium4 Xeon processors, with a speed of 355 gigaflops (billion floating point operations per second), to 98 processors in 2003. The current system has 98 gigabytes of memory, 10 terabytes of disk storage, and a 12-terabyte SDLT tape library. "Rocks has been exceptionally helpful in our cluster implementation," said Jim Simpson, the group’s principal investigator.

"The price-performance ratio we are getting out of our Rocks cluster is staggering," said Tim McIntire, lead programmer and system administrator. "We are able to process massive satellite data sets in several hours that used to require over a month."

University of Texas at Austin

The Center for Subsurface Modeling (CSM) in the Institute for Computational Engineering and Science (ICES) at the University of Texas at Austin uses the 90-processor "Bevo" cluster to model the behavior of fluids such as petroleum and water in permeable geologic formations and in shallow bodies of water.

"NPACI rocks is a fantastic way to administer a cluster," said ICES networking systems analyst Ari Berman. "The tools included in this package are full featured and make life for a system administrator easier. The most valuable aspect of Rocks is that the node installs are disposable, and reinstallation is extremely fast and easy. Additionally, the NPACI Rocks community has been extremely supportive and can usually answer any question via a mailing list."

The 44-processor "Jupiter" cluster at UT’s Institute for Advanced Technology is used to model and assess systems which are characterized by mechanically, thermally coupled electromagnetic diffusive processes with moving conductors such as pulsed rotating power supplies and electromagnetic launchers.

The 16-processor Pluto cluster at UT’s Institute for Advanced Technology is used to model ballistic and shock physics problems, and to analyze hypervelocity impact physics. "The Pluto cluster has had hardware and software errors of every kind," said system administrator Jared Hodge. "Finally, using Rocks and good systems administration procedures, we were able to track down the last of the hardware and software problems."

Hong Kong Baptist University

In early 2003 the was established at Hong Kong Baptist University (HKBU) with the support of Teaching Development Grants from the Hong Kong University Grants Committee, Dell Corporation (Hong Kong), Intel Corporation (Hong Kong), and the university’s Faculty of Science. The purpose of the facility is to provide teaching and research opportunities in parallel and distributed computing for students from various academic institutions in Hong Kong. Students learn how to compute in a parallel environment in laboratory demonstrations and exercises. Undergraduate students are using the PC cluster to work on senior-year projects. Research groups of professors, visiting scholars, and Ph.D. students are using the cluster to carry out projects in molecular modeling, Monte Carlo methods, statistical physics, and other areas.

“We had used Rocks successfully in a 16-node fast Ethernet Pentium III cluster,” said system administrator Morris M.M. Law. “When setting up our new 64-node gigabit Ethernet P4-Xeon cluster we were very pleased to be able to install Rocks on the master and slave nodes within two hours. We hope that Rocks can help us bring PC-cluster computing into the mainstream of our teaching and research here at HKBU.”

University of Macedonia, Greece

Students and staff in the Parallel Distributed Processing Laboratory within the Department of Applied Informatics at the University of Macedonia use the 65-processor “Electra” cluster to do performance modeling of scientific computations on heterogeneous systems, fault tolerance in scientific computations, parallel evolutionary computations, approximate string matching, and non-linear optimization. The server is also connected to the university’s backbone network, providing remote job submission and monitoring through the Internet from the lab’s Web site.

The nodes are slow, outdated PCs (100 to 233 MHz Pentium chips) that had been withdrawn from regular office and lab use. The interconnection network is a two-level tree structure of 100 Mbps Ethernet switches. The operating system software is based on Red Hat Linux, NPACI Rocks, and the Ganglia Toolkit.

“Before using NPACI Rocks we developed two smaller clusters with 8 to 16 nodes,” said system administrator Bill Stefanidis. “In retrospect, we think it would be impossible to implement a 65-node cluster without the help of Rocks, which proved quite easy to install, configure, use, and extend.”

University of South Carolina

The laboratory of Kevin Higgins, an assistant professor in the Department of Biological Sciences at the University of South Carolina, uses a cluster for computational research in population biology, to simulate the genetic and demographic mechanisms controlling the extinction of natural populations. A primary research goal is to identify the types of wildlife that may be particularly vulnerable to declines in population fitness due to the accumulation of deleterious mutations.

South Carolina’s "Extinction Machine" cluster consists of 97 dual-processor AMD Athlon nodes with a peak speed of 671 gigaflops connected by a Hewlett-Packard ProCurve 5372xl switch. "The Rocks parallel computing environment is extremely stable and provides all the tools needed for true high performance computing," said Higgins.

Texas Tech University

The High Performance Computing Center at Texas Tech currently manages and maintains four Beowulf clusters that use NPACI Rocks clustering software. Some researchers at the university use the clusters in computational chemistry calculations in serial and parallel, while other researchers calculate orbital forces between atoms.

Texas Tech has incorporated the clusters running NPACI Rocks into TechGrid, a campus-wide grid of Windows PC, Linux, and Unix systems with a single access point. Adding the Rocks systems to this Grid was relatively uncomplicated, said David Chaffin, administrator of the four Rocks clusters.

University of Tromsø, Norway

The "Snowstorm" cluster at the University of Tromsø’s High Performance Computing Project at the Computer Center is a general-purpose resource for scientists and students in Norway. It is part of the computing resources available to academic users from NOTUR, the national high-performance computing effort in Norway.

"We see a high demand for the cluster’s performance in fields like pharmacology and bioinformatics, both as a parallel computing engine and as a throughput machine running single-CPU jobs," said system administrator Roy Dragseth. "NPACI Rocks gave us a turnkey solution that worked out of the box. It was a real time-saver when we started with clusters and it has proven its stability and usability in our production environment with scientists and students running very demanding tasks. The fact that Rocks is based on standard Red Hat Linux makes it fit extremely well into our department’s other IT infrastructure."