| Title | Analysis and Optimization of a Molecular Dynamics Code using PAPI and the Vampir Toolchain |
| Publication Type | Conference Paper |
| Year of Publication | 2012 |
| Authors | William, T., D. K. Berry, and R. Henschel |
| Conference Name | Cray User Group 2012 |
| Date Published | 05/2012 |
| Publisher | CUG |
| Place Published | Stuttgart |
| Type of Work | Paper, Presentation |
| Keywords | molecular dynamics, MPI, OpenMP, tracing |
| Abstract | A highly diverse molecular dynamics program for the study of dense matter in white dwarfs and neutron stars was ported and run on a Cray XT5m using MPI, OpenMP and hybrid parallelization. The ultimate goal was to find the best configuration of available code blocks, compiler flags and runtime parameters for the given architecture. The serial code analysis provided the best candidates for parallel parameter sweeps using different MPI/OpenMP settings. Using PAPI counters and applying the Vampir toolchain a thorough analysis of the performance behavior was done. This step led to changes in the OpenMP part of the code yielding higher parallel efficiency to be exploited on machines providing larger core counts. The work was done in a collaboration between PTI (Indiana University) and ZIH (Technische Universitat Dresden) on hardware provided by the NSF funded FutureGrid project. |
| URL | https://cug.org/proceedings/attendee_program_cug2012/includes/files/pap142.pdf |
| Scope | external |
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