It’s not always easy for students to see what a molecule looks like based on an equation. An associate professor of chemistry at Sonoma State University recognized this, so he set out to show them.
By using supercomputers to calculate the properties of molecules, Mark Perri’s students could begin to visualize the meaning of the equations he wanted them to learn.
Simulating chemistry equations on supercomputers helps students visualize what they need to learn. But not all students have access to these resources. That's why Sonoma State University professor Mark Perri created the Chem Compute gateway to provide these visualizations for free.
“It basically provides a graph of the equation—a visualization of it for them,” Perri says. “A lot of students aren't mathematically minded. It doesn't light up in their minds in the same ways it does for us teachers, until they see it. But once they see it, then they can draw the connections and learn about it.”
The problem was, Sonoma State didn’t have a supercomputer, or access to one. There wasn’t even a small cluster to work with. Perri first bought a commercial package to do the calculations and render the visualizations, but the licensing costs were too high for his budget, and he could only afford to license one computer to do the calculations.
Despite these obstacles, Perri is a big believer in equity and equal access and he wasn’t willing to give up. He knew that other universities had the capabilities to run visualizations for their students.
“I think our students should have access to this as well,” said Perri. “I’m really focused on the fact that we can give our students the same access to these tools that a lot of other students already have.”
So Perri built his own cluster and a gateway website to work from. He linked four desktop computers together, each of which had four cores, so that gave him 16 cores to work with. At first, that was fine for his twenty undergraduates.
“Then I thought, well, if my students can do it, it’s just a website,” he said. “I might as well give access to the whole world. So I turned it on for everybody.”
And the Chem Compute science gateway was born.
Unfortunately, by opening it up to the world for free, Perri got a bit more than he bargained for. People started running complex simulations on his little homemade cluster, causing it to overheat.
Perri applied to the Extreme Science and Engineering Discovery Environment (XSEDE) for additional computing resources. As it happened, one of the application reviewers, Marlon Pierce of Indiana University, was also a member of the Science Gateways Community Institute (SGCI).
Pierce recognized that SGCI’s guidance and technical assistance could be of service to Perri in his pursuit to take Chem Compute further. With SGCI’s help, Perri got the technical help he needed to build his science gateway and additional computing resources from XSEDE (some of which he hadn’t even known to ask for).
“XSEDE has been great,” Perri said. “One of the best things about XSEDE is Jetstream. Jetstream gives you all these virtual machines, so it's like having a server on Amazon or Google, but it's free. On Jetstream, you can have whatever size virtual machine you need—and I can add more when I need them. Just the fact that Jetstream has free hosting has been awesome.”
XSEDE also gave Chem Compute access to the Bridges and Comet supercomputers to do the calculations. With more and more people using it for research purposes, instead of solely for teaching, it was necessary to bring in the heavies.
Since engaging with SGCI and getting the XSEDE resources he needs, Perri has seen a huge amount of growth in the number of Chem Compute users from all over the world. Traffic comes from as far afield as Yamaguchi University in Japan, and from big and small universities all over the US, from University of California, Davis (UC Davis) to Guilford College and Tuskegee University.
“My students love it when I have them use it, and so I think it's important,” Perri said. “I get emails from other faculty who say thank you because they don't have any other access to anything like this. I think it's important to keep it going.”