AWS HPC Blog

Tag: GROMACS

Running cost-effective GROMACS simulations using Amazon EC2 Spot Instances with AWS ParallelCluster

In this blog post, we cover how to run GROMACS – a popular open source designed for simulations of proteins, lipids, and nucleic acids – cost effectively by leveraging EC2 Spot Instances within AWS ParallelCluster. We also show how to checkpoint GROMACS to recover gracefully from possible Spot Instance interruptions.

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GROMACS performance on Amazon EC2 with Intel Ice Lake processors

We recently launched two new Amazon EC2 instance families based on Intel’s Ice Lake – the C6i and M6i. These instances provide higher core counts and take advantage of generational performance improvements on Intel’s Xeon scalable processor family architectures. In this post we show how GROMACS performs on these new instance families. We use similar methodologies as for previous posts where we characterized price-performance for CPU-only and GPU instances (Part 1, Part 2, Part 3), providing instance recommendations for different workload sizes.

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Running 20k simulations in 3 days to accelerate early stage drug discovery with AWS Batch

In this blog post, we’ll describe an ensemble run of 20K simulations to accelerate the drug discovery process, while also optimizing for run time and cost. We used two popular open-source packages — GROMACS, which does a molecular dynamics simulations, and pmx, a free-energy calculation package from the Computational Biomolecular Dynamics Group at Max Planck Institute in Germany.

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Figure 4: Relative price-to-performance ratio ($USD/ns) while scaling the simulation across single and multi-GPU instances and comparing to CPU (EFA enabled) performance-to-price (baseline CPU perf).

Running GROMACS on GPU instances: multi-node price-performance

This three-part series of posts cover the price performance characteristics of running GROMACS on Amazon Elastic Compute Cloud (Amazon EC2) GPU instances. Part 1 covered some background no GROMACS and how it utilizes GPUs for acceleration. Part 2 covered the price performance of GROMACS on a particular GPU instance family running on a single instance. […]

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Figure 4: Performance scaling as a function of CPU core count increase while number of GPU's remain constant.

Running GROMACS on GPU instances: single-node price-performance

This three-part series of posts cover the price performance characteristics of running GROMACS on Amazon Elastic Compute Cloud (Amazon EC2) GPU instances. Part 1 covered some background no GROMACS and how it utilizes GPUs for acceleration. This post (Part 2) covers the price performance of GROMACS on a particular GPU instance family running on a […]

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Figure 2: Work distribution across CPU and GPU for a single simulation timestep

Running GROMACS on GPU instances

Comparing the performance of real applications across different Amazon Elastic Compute Cloud (Amazon EC2) instance types is the best way we’ve found for finding optimal configurations for HPC applications here at AWS. Previously, we wrote about price-performance optimizations for GROMACS that showed how the GROMACS molecular dynamics simulation runs on single instances, and how it […]

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GROMACS price-performance optimizations header image

GROMACS price-performance optimizations on AWS

Molecular dynamics (MD) is a simulation method for analyzing the movement and tracing trajectories of atoms and molecules where the dynamics of a system evolve over time. MD simulations are used across various domains such as material sciences, biochemistry, biophysics and are typically used in two broad ways to study a system. The importance of […]

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