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March 10, 2010

Florida State Gives Virtual SMPs a Spin

by Michael Feldman

The prospects for virtual SMP technology got another boost last month when Florida State University (FSU) announced it had installed a new HPC system from 3Leaf Systems. The servers are being housed at the university’s HPC facility and will be used across a range of scientific disciplines. It represents the first announced shipment of 3Leaf’s virtual SMP offering.

A relative newcomer to the HPC space, 3Leaf launched its initial server product, called the “Dynamic Data Center Server” (DDC-Server) in November 2009. Using special hardware and software, it enables a set of x86 server nodes to be aggregated into one or more virtual SMP machines. The 3Leaf server shipping today is based on dual-socket Opteron motherboards supplied by Supermicro.

The idea is to provide a platform for applications that require high core count and/or high memory environments, but without the expense of a hard-wired SMP system. And since the aggregation is all done virtually, users can rejigger the SMP configuration on the fly to match different application needs. It’s basically having a cluster and eating it too.

In general, the 3Leaf technology mirrors that of competitor ScaleMP. Unlike ScaleMP though, which does all its virtualization magic in software, 3Leaf has devised a custom ASIC that manages cache coherency at the hardware level. Also unlike ScaleMP, the 3Leaf product is integrated with AMD Opteron-based motherboards. Currently, ScaleMP only supports Intel Xeon-based servers.

This actually turned out to be an important consideration for the university. Since FSU is primarily an AMD shop, sticking with Opteron hardware meant ruling out the ScaleMP solution. The other attraction to 3Leaf was the better promised performance for their ASIC-based cache coherency mechanism.

The new system at FSU is based on six-core Istanbul CPUs, and consists of 12 dual-socket servers connected over QDR InfiniBand. The system sports 576 GB of memory and 6 TB of disk storage. Of the 144 total cores, 138 are available to user apps, with the remainder dedicated to the operating system. Although FSU is not saying how much they paid for the servers, according to 3Leaf, the list price for a system this size is $206 thousand.

On top of the hardware is the resource allocation software. 3Leaf offers different variations of resource management, depending on how you want to slice and dice the servers. The software chosen by FSU was DDC-Pool, which can construct virtual SMP machines at the granularity of the cluster node. Also, with DDC-Pool, reconfiguration requires a system reboot. Obviously, this type of setup implies that it will be used for applications that run for a relatively long time before a reallocation of CPUs and memory is needed.

Since the new system is part of the university’s shared HPC facility, it’s intended to support any FSU researcher. Currently the facility supports about 450. Jim Wilgenbusch, who heads the shared HPC facilty at university, estimates around 25 percent of those users share a need for SMP-type systems with larger memory or larger numbers of CPU cores. To satisfy the demand, they’ve set up a “SMP queue” into which anyone can request a specific number of processors and memory footprint. As needed, the system’s CPUs and RAM are allocated to users as a virtual system and then released back into the resource pool when the application completes.

Wilgenbusch thinks the main application areas that will make good use of the SMP technology are astrophysics, earth and atmospheric science, and imaging applications. FSU recently received a large NIH grant for a cryo-electron microscope, which generates reams of 3-D images for post-processing. Wilgenbusch says that’s just the type of application well-suited to the 3Leaf platform, since it tends to need a much larger memory footprint than can be had on a single physical node.

Theoretically, one application could hog all 138 cores, but most of the user requests they’re getting are for allocations of 44 to 128 cores, with approximately 44 GB per core. As in most shared systems, the bigger the request, the longer the wait for resources.

The 3Leaf system marks a return to a fat node architecture for FSU. During the last decade, the HPC facility there contained a number of large SGI Altix and IBM Power-based SMP computers. These were phased out during the middle of the last decade and were replaced by HPC clusters. “The problem we had with the older systems was that it was very difficult to find a funding path for updating and maintaining that hardware unless it was acquired on a single-purpose special grant,” explains Wilgenbusch.

Today the bulk of the computing infrastructure at the shared HPC facility is a large (398-node) Dell PowerEdge cluster hooked together with DDR InfiniBand. These are used mainly for traditional MPI codes. University researchers also have access to a Condor system for high throughput-type jobs that don’t rely on tight coupling between nodes. The acquisition of the 3Leaf system gives the HPC facility that additional dimension for applications.

Wilgenbusch says their early experience with the 3Leaf product has been very positive. Once researchers get access to a large SMP cache-coherent environment, the first complaint is usually that they would like more of it. In the short term, he expects to expand the current system to 192 cores and around a terabyte of memory.

That sized system would max out the aggregation capability of the current 3Leaf offering. The company is planning to develop an Intel Xeon-based version, based on the future “Sandy Bridge” processors at some point. That technology will scale up to 32 nodes, hundreds of cores, and 64 TB of memory.

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