By Rose Bialk
On Monday, Nov. 11, Watzek Library hosted an event celebrating a recent upgrade to the college’s high-performance computing cluster, affectionately known as BLT for its worker nodes “Bacon,” “Lettuce” and “Tomato.”
Ben Glick ’20 is an alum who has been helping the school operate the cluster since its initial installation. He explained the nature of the network in his presentation at the event and emphasized its implementation on campus and beyond.
“We have had this system on campus since 2017. We have served four plus departments, five plus courses and multiple hemispheres. There was one project where Greta’s class used this system from Australia. That was kind of logistically fun to support, but it worked out pretty well, and now we can say we used it literally across the world,” said Glick. “We started the project in 2017 because we had some pressing bioinformatics needs where they just were not going to scale on any of the infrastructure we had.”
Bioinformatics describes a scientific subdiscipline concerned with analyzing and arranging sets of biological data. Due to the size of these datasets, this type of work often requires serious computational resources. When a student project exceeded the computational capacity of campus hardware, attempts to outsource the computing to Amazon Web Services turned out to be extremely expensive. Luckily, Amazon discounted the price for academic purposes,
Since the system’s installation in 2017, it has undergone three upgrades, adding a high-performance file storage system, named “Bread” and a graphics processing unit named “Sprouts.” A new set of two central processing units (CPUs) was also installed just before the presentation on Nov. 11. These new CPUs are named “Onion” and “Pickles.” Glick described how these newer CPUs from the company Advanced Micro Devices, Inc. (AMD) would drastically improve overall performance.
“Depending on how you count, anywhere between 66% and probably a couple hundred percent performance speed up on our system, because these two are top of the line AMD CPUs built in 2023, and all the other ones that we had are older Intel, kind of mid-range server CPUs, which were built in 2016 through 2018,” Glick said.
Joining Glick on the leadership team are Head of Digital Services at Watzek Library Jeremy McWilliams and Professor of Biology Greta Binford, who have been working on the project from the get-go. Binford’s work involves complex bioinformatics that the computing cluster can handle and LC was able to direct some funding toward filling this gap in research resources on campus, much more affordably than outsourcing to a cloud service.
The BLT recently finished a five-week computation analyzing Binford’s work, sorting an index of genetic sequences based on their similarities. The index contained 27 trillion base pairs. If it had been executed on a single computer core, where the average laptop might contain four cores, this computation would have taken 22 years, longer than many students have been alive for.
“What we really need now, as Jeremy and Greta alluded to, is engagement, especially outside of the sciences,” Glick said. “We have some number of hundreds of thousands of dollars worth of infrastructure downstairs that not that many people on campus even know exists, which is not that great. It definitely, like people have said, is a unique opportunity to have access to this kind of a system from a small school.”
For inquiries about or technical assistance using these powerful, recently-upgraded computers, email blt-cluster@lclark.edu.
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