GROMACS Performance on AMD Instinct MI355X

2026-03-13 · Source: AMD ROCm Blogs · Field: Technology & Digital — Artificial Intelligence & Machine Learning, Cloud Computing & IT Infrastructure, Data Science & Analytics · Depth: Intermediate, medium

Summary

AMD's latest Instinct MI355X GPU demonstrates significant performance improvements for GROMACS molecular dynamics simulations compared to its predecessor, the MI300X. Benchmarks using the ADH dodec system on a dual-socket server with 2x AMD EPYC 9654 CPUs and 8x GPUs show the MI355X achieving up to 10,300 ns/day throughput in Compute Partitioned (CPX) mode with 8 GPUs. This represents a 28% to 50% performance advantage over the MI300X, with the largest gain (49.9%) observed in a 2-GPU configuration. GPU partitioning itself provides substantial speedups, ranging from 1.7x to 3.2x on both MI300X and MI355X architectures for multidir workloads, which launch multiple independent simulation replicas in parallel.

Key takeaway

For AI Scientists and HPC researchers planning hardware upgrades for molecular dynamics, the AMD Instinct MI355X offers a compelling performance leap over the MI300X, delivering up to 50% faster GROMACS throughput. You should prioritize deployments utilizing GPU compute partitioning (CPX mode) to maximize simulation efficiency, as this configuration provides 1.7x to 3.2x speedups on both GPU generations, accelerating time-to-results for life-science research.

Key insights

AMD's MI355X GPU significantly boosts GROMACS molecular dynamics performance, especially with compute partitioning.

Principles

• GPU partitioning enhances throughput for parallel simulations.
• Newer GPU generations offer substantial performance gains.
• Scaling efficiency varies with GPU count and system resources.

Method

Benchmarking GROMACS with the ADH dodec system on AMD Instinct GPUs, comparing Single Partition (SPX) and Compute Partitioned (CPX) modes across 1 to 8 GPUs to measure ns/day throughput.

In practice

• Enable CPX mode for 1.7-3.2x GROMACS throughput gains.
• Consider MI355X for 28%+ performance over MI300X.
• Balance concurrent replicas for optimal performance.

Topics

• GROMACS
• Molecular Dynamics
• AMD Instinct MI3555X
• GPU Benchmarking
• Compute Partitioning

Best for: AI Scientist, Research Scientist, AI Engineer, AI Architect

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Editorial summary, takeaway, and curation by AIssential. Original article published by AMD ROCm Blogs.