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Gromacs adh_cubic Benchmark

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Gromacs公式ページにて紹介されているベンチマークテスト ADH_bench_systems の中で最も原子数の多いベンチマークテスト adh_cubic を実施した結果を御紹介します。adh_cubic は、134,177原子のベンチマークです。​表中の「ns/day」の値が大きいほど、パフォーマンスが高いことを示します。

coulombtype = PME

SIMD Test

​ハードウェアとソフトウェアの構成を一定にして、GromacsのSIMDに関するビルドオプションを変更して、ベンチマークを取得しました。CPUクロックは、OSのturbostatコマンドで取得したものの値の上限と下限を示しました。ベンチマークデータは、adh_cubic、coulombtype=PMEです。(2017/09)

coulombtype = Reaction-Field

OpenCL版 Gromacs における制限事項 ※以下、公式サイトから転載 (2018-08)

Limitations in the current OpenCL support of interest to GROMACS users:

  • No Intel devices (CPUs, GPUs or Xeon Phi) are supported

  • Due to blocking behavior of some asynchronous task enqueuing functions in the NVIDIA OpenCL runtime, with the affected driver versions there is almost no performance gain when using NVIDIA GPUs. The issue affects NVIDIA driver versions up to 349 series, but it known to be fixed 352 and later driver releases.

  • On NVIDIA GPUs the OpenCL kernels achieve much lower performance than the equivalent CUDA kernels due to limitations of the NVIDIA OpenCL compiler.

  • The AMD APPSDK version 3.0 ships with OpenCL compiler/runtime components, libamdocl12cl64.so and libamdocl64.so (only in earlier releases), that conflict with newer fglrx GPU drivers which provide the same libraries. This conflict manifests in kernel launch failures as, due to the library path setup, the OpenCL runtime loads the APPSDK version of the aforementioned libraries instead of the ones provided by the driver installer. The recommended workaround is to remove or rename the APPSDK versions of the offending libraries.

 

Limitations of interest to GROMACS developers:

  • The current implementation is not compatible with OpenCL devices that are not using warp/wavefronts or for which the warp/wavefront size is not a multiple of 32

  • Some Ewald tabulated kernels are known to produce incorrect results, so (correct) analytical kernels are used instead.

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