PAGE 4 OF 5
Janelia's IT team—Vijay Samalam, Spartaco Cicerchia, and Goran Ceric—recently updated its computing cluster, building it from commercially available hardware components by Intel, Dell, and Arista Networks, and using popular and now faster Ethernet networking.
Humans proofread the final fly-brain image for accuracy, to trace the neural paths and make sure the computer has identified structures correctly. “[People] are an important step,” says Winston. “Without them, the computer segmentation would be 95 percent right and we wouldn't know about the other 5 percent.”
Scheffer and Winston's ultimate goal is to completely automate the mapping process and to teach the computer to identify the inner structures of the fruit fly brain, in particular the different types of neurons, and the axons and dendrites branching out from them. “To do the whole fly brain we have to improve the automated segmentation,” says Winston. Scheffer hopes to achieve the computer-generated—and accurate—mapping of the brain within the next five years as more pieces are imaged and processed.
The increased speed of the new computing system will make that effort easier going forward. The cluster is faster than its predecessor for two reasons: it has more than four times as many individual processors, and it's using a networking technology that speeds up the communication between processors. Those familiar with office networks know it well: Ethernet, the popular standard for moving electronic data from point A to B. While it has been a longstanding protocol for slower connections, 10-gigabit Ethernet has not traditionally been the choice of makers and engineers of top supercomputers who until recently, when best performance was a must, used specialized networking technology called InfiniBand.
“Now Ethernet switches are as efficient as, or very close to, InfiniBand and you don't need a different [networking] skill set,” says Spartaco Cicerchia, manager of network infrastructure at Janelia Farm. The bottom-line advantage is that Ethernet is easier to work with, familiar to more networking engineers, and tends to be cheaper to use.
Lower latency—the time it takes to move data across a network connection—is now possible via Ethernet due to a relatively new networking standard called iWarp. Traditionally, computers' processors must manage the flow of information packets as they pass between them. In the new systems, those packets are handled by a separate piece of hardware made by the chip manufacturer Intel.
“Traditionally, [central processing units handle] network packets. However, when network interface speeds went from 1 to 10 gigabits per second, the load on CPUs increased by an order of magnitude,” says Goran Ceric, Janelia's manager of scientific computing systems.
The creation of iWarp helped alleviate this issue and reduce latency and overhead. iWarp helps in three ways, according to Ceric: by processing network packets using specialized hardware instead of CPUs; by placing data directly into application buffers, thus eliminating intermediate packet copies; and by reducing a need for “context switching,” in which a processor must pass commands back and forth between an application and an operating system. “For many parallel applications,” he says, “if you can lower communications time between processors in different systems over the network, the better your performance is.”
The new network infrastructure has dropped the communications lag inside the Janelia cluster from 60 to 10 microseconds—a sixfold improvement.
Janelia Farm fellow Roian Egnor isn't a computer scientist or network engineer, but her research on the vocalizations of mice (and the neural pathways required) depends partly on heavy computation power. Though famed for their quiet ways, it turns out mice are chatterboxes. All their communications, unfortunately, happen at frequencies between 30 and 100 kilohertz, far above the range of human hearing.
“There's a secret world up there,” says Egnor, who records hours of mouse talk daily. “If you take those vocalizations and computationally lower frequencies, they sound remarkably like bird songs.”
Photo: Paul Fetters