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Talk- John Eblen

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GROMACS: Computing in the Gap

What
  • cmb seminar
When Feb 19, 2018
from 11:00 AM to 12:30 PM
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One way to improve software performance is to seek out "gaps," or times when computing resources are idle, and fill those gaps with useful work. In this talk, I'll discuss our efforts to improve the performance of GROMACS MD simulations by computing forces inside gaps that occur when processes communicate. These "communication gaps" happen when processes (MPI processes) stop to share data. This sharing only requires a single thread (compute core) from each process. Thus, the remaining threads become idle. We seek to fill these gaps by carefully scheduling work for each thread between simulation steps. I'll discuss the main challenges, such as figuring out how to divide work more finely and how to deal with varying gap sizes. I'll discuss our progress and the challenges that remain.

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