From Science Node: “Supercomputing sister sites”

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Science Node

03 May, 2017
Kirsten Gibson

Juan Carlos Vergara used to have go two weeks at a time without his personal computer while it was busy modeling earthquakes. Then he found Apolo.

Long-distance relationship. Purdue University and EAFIT have teamed up to bring supercomputing to Colombia. Here, Gerry McCartney and Donna Cumberland from Purdue University discuss Apolo with Juan David Pineda from EAFIT. Courtesy Purdue University, EAFIT.

Apolo, the first research supercomputer at the Universidad EAFIT in Medellin, is the fruit of a partnership between Purdue University’s research computing unit and the Apolo Scientific Computing Center.

With Apolo, Vergara finishes his work in days instead of months, and can expand the scale of his simulations five million times.

With Apolo comes a staff to run it, including Juan David Pineda, Apolo’s technology coordinator, and Mateo Gomez, a high-performance computing (HPC) analyst.

“Sometimes we would be up until 1am helping me solve problems,” says Vergara, a doctoral student of applied mechanics at EAFIT. “I saw them as part of my team, fundamental to what I do every day.”

For their part of the partnership, Purdue brought a lot of experience accelerating discoveries in science and engineering. Purdue’s central information technology organization has built and operated nine HPC systems for faculty researchers in as many years, most rated among the world’s top 500 supercomputers.

Hardware from one of those machines, the retired Steele cluster, became the foundation of Apolo.

Steele cluster

People powered

While the hardware is important, the partnership is more about people. Purdue research computing staff have traveled to Colombia to help train and to work with EAFIT colleagues. EAFIT students have participated in Purdue’s Summer Undergraduate Research Fellow (SURF) program working with many supercomputing experts.

EAFIT and Purdue have also sent joint teams to student supercomputing competitions in New Orleans and Frankfurt, Germany. Some of the Colombian students on the teams have become key staff members at the Apolo center, which, in turn, trains the next generation of Colombia’s high-performance computing experts.

Juan Luis Mejía, rector at Universidad EAFIT, says EAFIT had been searching for an international partner to help reverse decades of isolation. What it found in Purdue was unexpected.

“Finding an alliance with a true interest in sharing knowledge of technology and without a hidden agenda allows us to progress,” Mejía says. “I believe that the relationship between our university and Purdue is one of the most valuable.”

Quantum leap

Because of the partnership with Purdue, Apolo has enabled research ranging from earthquake science, to a groundbreaking examination of the tropical disease leishmaniasis, to the most ‘green’ way to process cement, to quantum mechanics – in all cases, Apolo accelerates EAFIT researchers’ time to science.

And since EAFIT is one of the few Colombian universities with a supercomputer and a strong partnership with a major American research university, it is poised to receive big money from the Colombia Científica program.

EAFIT has already attracted the attention of Grupo Nutresa, a Latin American food processing company headquartered in Medellín, and researchers like Pilar Cossio, a Colombian HIV researcher working for the Max Planck Institute in Germany.

When Cossio came home to Colombia after studying and working in Italy, the US, and Germany, the biophysicist figured that one big task she was going to face would be building her own supercomputer and finding someone to run it.

But thanks to the partnership with Purdue, she conducts her research at the Universidad de Antioquia in Medellín with help from the Apolo Scientific Computing Center at EAFIT.

Cossio’s research combines physics, computational biology, and chemistry. She’s studying protein changes at the atomic level which can help design drugs to cure HIV. That endeavor requires examining around two million different compounds to see which ones bind the best with particular proteins.

“There are only two supercomputers in Colombia for bioinformatics,” Cossio says. “Apolo is the only one that focuses on satisfying scientific needs. It’s important for us in the developing countries to have partnerships with universities that can help us access these crucial scientific tools.”

As it is for many scientists, high-performance and parallel computing power are vital for her research — she just didn’t anticipate finding a ready-made solution in her home country.

Then she found Apolo.

See the full article here .

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