Performance analysis of a parallel molecular dynamics program

Performance analysis of a parallel molecular dynamics program

EGO is a parallel molecular dynamics program running on Transputers. We conducted a performance analysis of the EGO program in order to determine whether it was effectively using the computational resources of Transputers. Our first concern was whether communication was overlapped with computation,...

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Veröffentlicht in:Computer physics communications 1994, Vol.78 (3), p.265-278
Hauptverfasser: Sinha, Amitabh B., Schulten, Klaus, Heller, Helmut
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Sprache:eng
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Computational techniques
Exact sciences and technology
Mathematical methods in physics
Molecular dynamics and particle methods
Physics
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container_title Computer physics communications
container_volume 78
creator Sinha, Amitabh B.
Schulten, Klaus
Heller, Helmut
description EGO is a parallel molecular dynamics program running on Transputers. We conducted a performance analysis of the EGO program in order to determine whether it was effectively using the computational resources of Transputers. Our first concern was whether communication was overlapped with computation, so that the overheads due to communication not overlapped with computation were less. With the assistance of performance tools such as UPSHOT, and with instrumentation of the EGO program itself, we were able to determine that only 8% of the execution time of the EGO program was spent in non-overlapping communication. Our next concern was that the MFLOPS rating of the EGO program was 0.25 MFLOPS, while the Transputers have a sustained rating of 1.5 MFLOPS. We measured MFLOPS ratings of small blocks of OCCAM code and determined that they matched the performance of the EGO code.
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subjects Computational techniques
Exact sciences and technology
Mathematical methods in physics
Molecular dynamics and particle methods
Physics
title Performance analysis of a parallel molecular dynamics program
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