University at Buffalo’s Center for Computational Research
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Creating a holistic geoscientific model is complicated enough. So when scientists have to debug their computer code, they turn to Allinea DDT, a tool easy enough for undergraduates to use. ...

Creating a holistic geoscientific model is complicated enough. So when scientists have to debug their computer code, they turn to Allinea DDT, a tool easy enough for undergraduates to use.

“People were impressed with the results Christine achieved using Allinea DDT and assumed she was a highly educated computer science technician; whereas, at the time, I think she might have taken just one ‘intro to computer science’ course.” – Dr. Shawn Matott, computational scientist, University at Buffalo’s Center for Computational Research.

Read more at http://www.allinea.com/case-studies/

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University at Buffalo’s Center for Computational Research Document Transcript

  • 1. Case Study: Allinea DDT Helps Drive the Evolution of Geoscientific Model Development Snapshot Client: The University at Buffalo’s Center for Computational Research (CCR) is one of the leading academic supercomputing sites in the U.S. Challenge: To gain a more holistic view of the planet, environmental scientists and engineers are linking their models together and bringing in more data. The size, complexity and distributed nature of their projects make the traditional methods of debugging ineffective. Time and budget constraints make the problem seem insurmountable. Solution: Allinea DDT – the leading graphical debugging tool – makes it easy to debug a complex, multi-tiered project. Results: A new framework for debugging geosciences projects was created with the help of an undergraduate math major, who had such a positive experience with Allinea DDT she is switching her discipline to computer science. Summary quote: “People were impressed with the results Christine achieved using Allinea DDT and assumed she was a highly educated computer science technician; whereas, at the time, I think she might have taken just one ‘intro to computer science’ course.” – Dr. Shawn Matott, computational scientist, University at Buffalo’s Center for Computational Research. Creating a holistic geoscientific model is complicated enough. So when scientists have to debug their computer code, they turn to Allinea DDT, a tool easy enough for undergraduates to use. When it comes to modeling the Earth, we aren’t in the Garden of Eden anymore. The days are gone when a scientist could run a single model that works for a collected dataset and then publish the results. Today’s teams of geoscientists, hydrologists, and engineers are using supercomputers to link their models together and create experiments that are ever-more complex. “You want to get a large-scale holistic picture,” says Dr. Shawn Matott, computational scientist at the Center for Computational Research (CCR). “So, you want the best-trained person making the model for groundwater, and you also want to see what is happening with the fish population, human cancer rates, and so on. You’ve got to be able to link these different disciplines as represented by the computer models.” CCR has 8,000 cores capable of more than 100 teraflops. The center’s system is heterogeneous: 384 cores have access to GPUs while others can access large memory stores. As scientific models become more sophisticated, so must the tools for finding and solving errors. To this end, CCR uses Allinea DDT, the most advanced debugging tool available for scalar, multi-threaded and large-scale parallel applications. Allinea DDT is designed to make solving even the most complex multi-process, software problems straightforward. “You might have a model that runs in parallel on a CUDAenabled GPU, and then the optimizer runs in parallel using MPI,” says Matott. “You need tools that can manage that kind of complexity.” Christine Baxter, undergraduate student Dr. Shawn Matott, computational scientist University at Buffalo’s Center for Computational Research University at Buffalo’s Center for Computational Research
  • 2. Case Study: Allinea DDT Helps Drive the Evolution of Geoscientific Model Development Overcoming Time and Budget Constraints Compute program, funded by the National Science Foundation. Students work 15 hours a week on a research project alongside their regular courses. Time and budget constraints add even more challenges. Organizations like CCR need a debugging tool that is both robust and easy to use. Matott had four undergraduate math students, two from the University at Buffalo and two from Buffalo State College. He met with the group once a week to talk about their progress and answer questions. “You really can’t afford to stick a PhD or Master’s student on something like debugging code, because their expertise lies more in the science side of bringing these models together, building a better optimizer or better algorithms,” says Matott. He often finds assistants through the Undergraduate Research Group Experience, or URGE to The group tested five different optimizing algorithms on 15 different test functions, generating 200,000 simulations. Not all of the experiments ran successfully. Matott trained undergraduate Christine Baxter to write Bash scripts to isolate roughly 1,000 simulations that failed and then let her loose on Allinea DDT to debug several thousand lines of code. She discovered the bug in the sort function of one algorithm. “She had two weeks of training on Bash scripting, and basically no training on Allinea DDT. I just told her how to launch the software and, working through the GUI, she was able to figure it out,” says Matott. “I think if she’d had to use one of the commandline debuggers, it would have meant another two weeks of training to get her up to speed.” Once Baxter completed the debugging, she and Matott constructed the idea of a framework, which generalized her process so other computational scientists could benefit from it. Center for Computational Research Machine Room in the NYS Center of Excellence in Bioinformatics and Life Sciences
  • 3. Case Study: Allinea DDT Helps Drive the Evolution of Geoscientific Model Development Positive Experience with Allinea DDT Inspires Undergraduate It was a heady experience for an undergraduate to contribute to the evolution of geoscientific model development. Baxter took the debugging framework to the fall meeting of the American Geophysical Union with 25,000 attendees, where she displayed and defended her results in a poster session. “Here were these undergraduates standing sideby-side with professors, PhD students, and post-docs. People were impressed with the results Christine achieved using Allinea DDT and assumed she was a highly educated computer science technician; whereas, at the time, I think she might have taken just one ‘intro to computer science’ course,” says Matott. Baxter had such a positive experience using Allinea DDT and developing the debugging framework, she decided to switch majors from math to computer science. Center for Computational Research’s Computer Visualization Laboratory Ease-of-Use Makes Scientists More Independent As for the future of the debugging framework, Matott says he is considering publishing a paper along with a case study of Baxter’s experience. He may even write a software package to help geoscientists implement the debugging framework. In the meantime, he’s looking forward to trying out Allinea MAP , a performance analysis tool that uses the same interface as Allinea DDT. Matott says he could benefit from MAP’s problems-at-aglance approach. He’s also keen on the tool because part of his job is to help other researchers run their experiments on the supercomputing cluster. “Right now I have a lot of meetings with the users. If they are in a different discipline, they often need to train me about their area of study before I can help them,” says Matott. “It would be nice if I could turn them loose on a product as user-friendly as Allinea DDT. They could independently find out where in the code they’re spending all their time and we could take it from there.” Allinea DDT and Allinea MAP combine robust capability with unmatched ease-of-use so that scientists like Shawn Matott can focus on grand challenges like pushing the evolution of geosciences modeling so we can make better decisions about managing planet Earth.
  • 4. the environment Allinea Software Inc. 2033 Gateway Pl Ste. 500, San Jose, CA. 95110 USA Tel: +1 (408) 884 0282 www.allinea.com • info@allinea.com Allinea Software Ltd. The Innovation Centre, Warwick Technology Park, Gallows Hill, Warwick CV34 6UW UK Tel: +44 (0)1926 623 231 Fax: +44 (0)1926 623 232 For more information about the Allinea environment, visit www.allinea.com