Trestles is available to users of the TeraGrid, the nation’s largest open-access scientific discovery infrastructure. The system is among the five largest in the TeraGrid repertoire, with 10,368 processor cores, a peak speed of 100 teraflop/s, 20 terabytes memory, and 38 terabytes of flash memory. One teraflop (TF) equals a trillion calculations per second, while one terabyte (TB) equals one trillion bytes of information.
“Trestles is appropriately named because it will serve as a bridge between SDSC’s unique, data-intensive resources available to a wide community of users both now and into the future,” said Michael Norman, SDSC’s director.
Configured by SDSC and Appro, Trestles is based on quad-socket, 8-core AMD Magny-Cours compute nodes connected via a QDR InfiniBand fabric. Each of its 324 nodes has 32 cores, 64 gigabytes (GB) of memory, and 120 GB of flash memory. Debuting at #111 on the top 500 list of supercomputers in the latest ranking, Trestles will work with and span the deployments of SDSC’s recently introduced Dash system and a larger data-intensive system named Gordon, to become operational in late 2011.
“UCSD and SDSC are pioneering the use of flash in high-performance computing,” said Allan Snavely, associate director of SDSC and a co-PI for the new system. “Flash disks read data as much as 100 times faster than spinning disk, write data faster, and are more energy-efficient and reliable.”
“Trestles, as well as Dash and Gordon, were designed with one goal in mind, and that is to enable as much productive science as possible as we enter a data-intensive era of computing,” said Richard Moore, SDSC’s deputy director and co-PI. “Today’s researchers are faced with sifting through tremendous amounts of digitally based data, and such data-intensive resources will give them the tools they need to do so.”
Moore added that that Trestles offers modest-scale and gateway users rapid job turnaround to increase researcher productivity, while also being able to host long-running jobs. Speaking of speed, SDSC and Appro brought Trestles into production in less than 10 weeks from initial hardware delivery. “We committed to getting the system in the hands of our users and meeting NSF’s production deadline,” noted Moore.
Early User Successes
Early users of SDSC’s Trestles include Bridget Carragher and Clint Potter, directors at the National Resource for Automated Molecular Microscopy at The Scripps Research Institute in La Jolla, Calif. Their project focuses on establishing a portal on the TeraGrid for structural biology researchers to facilitate electron microscopy (EM) image processing using the Appion pipeline, an integrated, database-driven system.
"We are very excited about this early opportunity to use the Trestles infrastructure for high performance structural biology projects,” said Carragher. “Based on our initial experience, we are optimistic that this system will have a dramatic impact on the scale of projects we can undertake, and on the resolution that can be achieved for macromolecular structure.”
Another early user is Ross Walker, an adjunct assistant professor of chemistry at UC San Diego and an assistant research professor with SDSC specializing in computational chemistry. “Typically, computational chemists need only a moderate number of cores, between 128 and 512, for longer periods of time,” he said. “This is exactly what Trestles was designed to offer.”
Walker’s group recently ran some simulations of the Adenovirus Protease, a key enzyme in Adenovirus replication and an interesting drug target for severe upper respiratory and stomach infections which now have no remedy other than aspirin or some other anti-inflammatory.
Those calculations ran on 512 cores each, and the group was able to leave them running on Trestles almost unattended for two weeks. “Such 'hands-off' supercomputing greatly increases the productivity of my research team,” noted Walker.
To ensure that productivity on Trestles remains high, SDSC will adjust allocation policies, queuing structures, user documentation, and training based on a quarterly review of usage metrics and user satisfaction data. Trestles, along with SDSC’s Dash and Triton Resource clusters use a matrixed pool of expertise in system administration and user support, as well as the SDSC-developed Rocks cluster management software. SDSC’s Advanced User Support has already established key benchmarks to accelerate user applications, and subsequently will assist users in tuning and optimizing applications for Trestles. Full details of the new system can be found at http://www.sdsc.edu/us/resources/trestles/ .
Walker’s team also recently ran a significant number of quantum geometry optimizations in support of a new force field it is developing for molecular dynamics, taking advantage of Trestles’ generous amount of memory and symmetric multiprocessing (SMP) cores, along with its streamlined scheduler policy. “We were able to get these runs completed in only a few days on Trestles.”
Trestles’ size, allocation range, and scheduling practicesare expected to also benefit the emerging Science Gateway paradigm for high-performance computing system access. Science gateways are a relatively recent phenomenon in supercomputing. Currently led by Nancy Wilkins-Diehr of SDSC, the TeraGrid Gateway program began in 2004 as web portals designed and used by scientists. The program extends the analysis capabilities of these community-designed interfaces through the use of supercomputers, yet insulates users from supercomputing complexities.
During the final quarter of 2010, gateway users represented 42% of all researchers who ran jobs on the TeraGrid during that period, reflecting a steady growth in the number of users accessing high-end resources. Trestles’ policies are designed to meet the needs of that increasing user base.
NSF’s award to build and deploy Trestles was announced last August by SDSC, and Trestles will be available to TeraGrid users through 2013. In November 2009, SDSC announced a five-year, $20 million grant from the NSF to build and operate Gordon, the first high-performance supercomputer to employ a vast amount of flash memory. Dash, a smaller prototype of Gordon, was deployed in April 2010. All these systems are being integrated by Appro and use a similar design philosophy of combining commodity parts in innovative ways to achieve high-performance architectures.
Jan Zverina | Newswise Science News
UT professor develops algorithm to improve online mapping of disaster areas
29.11.2016 | University of Tennessee at Knoxville
New standard helps optical trackers follow moving objects precisely
23.11.2016 | National Institute of Standards and Technology (NIST)
A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.
Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...
In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.
“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...
The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.
The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...
Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water
In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...
The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.
Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...
16.11.2016 | Event News
01.11.2016 | Event News
14.10.2016 | Event News
02.12.2016 | Medical Engineering
02.12.2016 | Agricultural and Forestry Science
02.12.2016 | Physics and Astronomy