[gmx-developers] Test case for single node

Guido Giuntoli guido.giuntoli at huawei.com
Mon Feb 1 17:34:32 CET 2021


I am searching for representative input cases for GROMACS for performance evaluation.

The selection criteria is centered on (priority order):

1.       inputs that are good representatives for the GROMACS  user community

2.       desirable to run in a single node (approx. 96 ARM cores / CPU-only) in no more than 1 hour

3.       makes good use of the memory system and exploits well the SIMD units (NEON and possibly SVE)

Currently I have in mind 2 inputs cases:

1.       The "ion channel" that belongs to the Unified European Applications Benchmark Suite (UEABS). This input seems to be a good representative for the industry of proteins and polymer simulation (https://hpc.nih.gov/apps/gromacs/).

2.       The "nonbonded-benchmark" which is integrated inside GROMACS. The benchmark would allow analyzing different problem sizes and internal kernels (https://manual.gromacs.org/documentation/current/onlinehelp/gmx-nonbonded-benchmark.html).

I would appreciate some guidance or feedback about these two inputs cases and suggestions for considering. Are there good representatives of what the community normally use when they run GROMACS? Are there special parameters (such as time steps or problem size, etc.) to take into account for finally saying that the simulations are good examples of normal GROMACS executions?

Best regards | Mit freundlichen Grüßen

Guido Giuntoli
Software Solution Architect for Advance Computing

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