NIH revs up supercomputer

The National Institutes of Health is cranking up its homegrown LOBOS supercomputer to
Gigabit Ethernet rates to connect hundreds of nodes in the massively parallel system.

LOBOS, which stands for lots of boxes on shelves, is a Beowulf-class supercomputer
built in-house in 1997 to do molecular modeling for the Computational Biophysics Section
of the National Heart, Lung and Blood Institute. Like other Beowulf-class machines, it
consists of off-the-shelf desktop computers strung together to share large computing jobs.

LOBOS’ 164 Pentium II and Pentium Pro dual-processor nodes until now have been
linked by a Fast Ethernet ring, which initially was more cost-effective [GCN, Aug. 24, 1998, Page 53]. But recent reductions
in the cost of Gigabit Ethernet network interface cards and switches have changed the
balance, said staff scientist Eric Billings, head of the LOBOS project.

“The cost of a Gigabit NIC has come down by at least 40 percent, and the cost of
the port has come down more than that,” he said. The Gigabit Ethernet hardware also
may have a longer life than Fast Ethernet hardware.

“When we upgrade a box, we will pull out the Gigabit NIC and use it in the next
generation,” Billings said. “Amortized that way, it becomes even more

The institute’s CoreBuilder 9000 switch from 3Com Corp. of Santa Clara, Calif.,
will anchor 100 new Pentium Pro PCs with dual 450-MHz processors from Soft-Hard Systems of
Los Angeles.

Each node will have a Fast EtherLink XL PCI NIC from 3Com. Sixteen desktop boxes
initially were connected through the switch’s Gigabit Ethernet ports, and the rest
were linked via a 100-Mbps Fast Ethernet. Eventually all nodes will have Gigabit Ethernet
connections, Billings said.

The CoreBuilder modules and 3Com NICs used in LOBOS have a retail value of $134,150, he

Fast Ethernet switching cost about $250 per port and NIC in the earlier LOBOS
generations, compared with about $1,800 for Gigabit Ethernet at that time.

The PCs’ PCI buses transferred data between processors and peripherals at 135
Mbps, minimizing any performance boost from a Gigabit Ethernet upgrade.

Falling prices and PCI 2.1 buses in new desktop PCs should double the transfer rate.
Billings said LOBOS eventually could expand to as many as 256 dual-processor nodes, and
the boxes probably will get an upgrade about once a year. He expects the Gigabit Ethernet
NICs to last for several more PC generations as PCI bus speeds increase.

The original LOBOS ring topology connected only adjacent nodes. Under the new topology,
all data to and from the processors will pass through the switch, which has a fully
redundant star-wired interconnect, 43 Gigabit Ethernet ports and 40 Fast Ethernet ports.

The CoreBuilder 9000 can support up to 126 Gigabit Ethernet ports, and its backplane
has potential aggregate switching capacity of 560 Gbps. It allows setup of virtual LANs,
which could process multiple LOBOS jobs simultaneously.    

About the Author

William Jackson is a Maryland-based freelance writer.


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