Best CPU, GPU, and RAM for RELION Cryo-EM [ Updated ]

By Mark Stevens
April 1, 2024
cryo-em relion benchmarks Benchmarks

BIZON RELION GPU accelerated systems for Cryo-EM
BIZON RELION GPU workstations for Cryo-EM

RELION (REgularised LIkelihood OptimisatioN), a pivotal software in the world of Cryo-Electron Microscopy (Cryo-EM), stands at the crossroads of advanced computational methods and groundbreaking biological discoveries. This open-source software, developed at the MRC Laboratory of Molecular Biology, is instrumental in transforming vast amounts of raw Cryo-EM data into detailed, interpretable molecular structures. The driving force behind RELION’s efficiency and accuracy is its seamless integration with GPU (Graphics Processing Unit) computing, marking a significant leap in the speed and precision of biomolecular analysis.

This article aims to explore the intricate relationship between RELION and GPU technology. We will benchmark various NVIDIA GPU models to evaluate their performance in RELION and offer comprehensive guidance on configuring the optimal GPU workstation and server for Cryo-EM research. This deep dive will not only highlight the technical aspects but also shed light on the practical implications for scientists in the field of molecular biology.

This article dives into the best CPU, GPU, and RAM options for running RELION, focusing on the latest advancements in technology that cater to the specific needs of Cryo-EM data processing.

Understanding RELION: A Software Summary

RELION, an acronym for REgularised LIkelihood OptimisatioN, stands as a beacon in the Cryo-EM community for its robust image processing and 3D reconstruction capabilities. Originating from the need to analyze the complex data generated by Cryo-EM, RELION uses a Bayesian approach to iteratively refine 3D structures of biomolecules. This method sets it apart, offering both precision and reliability in the data it processes.

Since its inception, RELION has undergone numerous enhancements, each iteration bringing more sophistication and speed to its processing abilities. Notably, RELION's adoption of GPU computing has been a game-changer. By leveraging the parallel processing power of GPUs, RELION has significantly reduced the time required for complex computational tasks, such as 3D classification and high-resolution refinement, making it a preferred choice for researchers and scientists globally.

The software is designed to be user-friendly, with a focus on providing accurate results even for users who may not be experts in computational methods. Its flexible nature allows it to cater to a wide range of Cryo-EM projects, from academic research to more advanced commercial applications in pharmaceuticals and biotechnology. The combination of its accessibility, efficiency, and accuracy has made RELION a cornerstone in the field of structural biology and Cryo-EM.

GPU Support in RELION

One of the most significant advancements in RELION has been its integration with GPU computing. This leap forward was driven by the need to handle the ever-increasing data sizes and complexity of structures analyzed in Cryo-EM. GPUs, with their ability to perform parallel processing, have proven to be exceptionally suited for this task, enabling faster and more efficient data processing than traditional CPUs alone.

RELION leverages the power of NVIDIA CUDA, a parallel computing platform and programming model developed by NVIDIA. CUDA allows RELION to distribute its computation across thousands of GPU cores, drastically reducing the time for image processing and analysis. This integration has not only accelerated the workflow of Cryo-EM but has also opened doors to analyzing more complex structures and conducting research that was previously deemed time-prohibitive.

Compatibility with various NVIDIA GPUs is a key feature of RELION. From the more accessible GeForce series to the powerful and robust Tesla and Quadro lines, RELION is designed to harness the capabilities of a broad spectrum of NVIDIA GPUs. This flexibility ensures that both academic institutions with limited budgets and high-end research facilities can utilize RELION effectively. The software regularly updates its compatibility to include the latest advancements in GPU technology, ensuring that users can continually benefit from the latest in speed and efficiency.

Best GPU for RELION Cryo-EM

Graphics Processing Units (GPUs) are at the heart of Cryo-EM data processing, significantly reducing computation times for tasks such as 3D classification and refinement. NVIDIA, a leading manufacturer of GPUs, offers several models that are well-suited for RELION. Let's explore the top contenders:

  • NVIDIA RTX 4090: The RTX 4090 is NVIDIA's flagship model, offering unparalleled performance. It features an impressive array of CUDA cores and a substantial amount of memory bandwidth, which is crucial for handling large Cryo-EM datasets. Its advanced architecture allows for efficient parallel processing, making it an ideal choice for demanding Cryo-EM computations. The RTX 4090's capability to handle multiple tasks simultaneously without a significant drop in performance is particularly beneficial for running multiple RELION jobs.

  • NVIDIA RTX 6000 Ada: Specifically designed for professional workstations, the RTX 6000 Ada is another excellent choice for Cryo-EM. It balances raw computational power with a larger memory size, making it suitable for processing extensive datasets that are typical in Cryo-EM studies. Its reliability and stability are key for long computation runs, a common scenario in Cryo-EM data processing.

  • NVIDIA RTX 5000 Ada: As a more cost-effective solution, the RTX 5000 Ada still delivers robust performance for RELION applications. It offers a good balance between computational power and memory size, making it a viable option for labs with tighter budgets. While it may not match the RTX 4090's raw power or the RTX 6000 Ada's workstation-grade reliability, it provides substantial capabilities for a wide range of Cryo-EM work.

In terms of the best GPU for RELION, the choice largely depends on your specific needs and budget. The RTX 4090 stands out for its sheer performance and is ideal for those who prioritize speed and are working with exceptionally large datasets. The RTX 6000 Ada offers reliability and ample memory for complex datasets, making it suitable for high-stakes projects that require consistent long-term computation. For those looking for a balance between cost and performance, the RTX 5000 Ada is an excellent choice.

Best CPU for RELION Cryo-EM

While GPUs handle the bulk of parallelizable tasks in RELION, the Central Processing Unit (CPU) remains critical for overall system balance and handling tasks that are not offloaded to the GPU. A high-performance CPU ensures that the GPU is fed with data efficiently, avoiding computational bottlenecks.

  • AMD Threadripper PRO: With multiple cores and threads, AMD's Threadripper PRO series is excellent for multitasking and parallel computations, characteristics beneficial for the data preprocessing stages in RELION.
  • Intel Xeon Scalable Processors: Intel's Xeon series offers robust performance, especially in configurations optimized for scientific computing. Its reliability and support for extensive memory capacities make it a solid choice for Cryo-EM data processing.

Storage & Memory/RAM for RELION Cryo-EM

The amount of data generated and processed in Cryo-EM studies is vast, making storage capacity and speed, as well as RAM, critical components of an efficient Cryo-EM computing setup.

  • RAM: For RELION, having a minimum of 128GB of RAM is recommended, but 256GB or more is ideal for handling large datasets and complex computations without bottlenecks.
  • Storage: High-speed SSDs (Solid State Drives) are crucial for fast data access and transfer. NVMe SSDs offer the best performance, significantly reducing the time required for reading and writing large data files. A combination of high-capacity HDDs (Hard Disk Drives) for long-term storage and SSDs for active projects provides a balanced and cost-effective storage solution.

Performance Benchmarking: NVIDIA GPUs in Focus

In the pursuit of optimizing RELION for Cryo-EM data analysis, understanding the performance of various NVIDIA GPU models is crucial. Given the diverse range of GPUs available, benchmarking their performances helps in identifying the most suitable options for different research needs and budget constraints.

The benchmarking process involves running standard sets of Cryo-EM data through RELION on different NVIDIA GPU models. This includes entry-level GPUs like the GeForce series, mid-range GPUs like the RTX series, and high-end options like the Tesla and Quadro models. Key performance metrics include the speed of image processing, the accuracy of 3D reconstructions, and overall computational efficiency.

Initial findings reveal distinct performance tiers. The GeForce series, while being the most affordable, generally shows longer processing times, making them suitable for smaller or less time-sensitive projects. The RTX series offers a significant leap in performance, balancing cost and computational power, which is ideal for mid-range applications. At the top tier, Tesla and Quadro GPUs deliver unparalleled speed and efficiency, albeit at a higher cost, making them a go-to choice for high-end, large-scale Cryo-EM projects.

The specific models within each series also show varied performances. For instance, within the RTX series, higher-end models like the RTX 4080 and 4090 demonstrate quicker processing times.

relion benchmarks
RELION Cryo-EM Benchmarks

In addition to these core components, factors like a fast SSD for storage, a robust cooling system, and a reliable power supply unit are also important in building a workstation that can handle the demands of Cryo-EM research. The ideal workstation is one that not only performs efficiently under heavy workloads but also offers scalability for future upgrades as GPU and CPU technologies continue to evolve.

Recommended GPU Workstations and Server for Cryo-EM

  • Recommended 2x GPU Cryo-EM NVIDIA GPU workstations: BIZON G3000, BIZON X5500

  • Recommended 4x GPU Cryo-EM NVIDIA GPU workstation (water-cooled): BIZON ZX5500
  • Recommended GPU server for Relion Cryo-EM: x7000


Understanding the real-world application and effectiveness of different GPU setups in Cryo-EM research is best illustrated through case studies and user experiences. These accounts provide valuable insights into how different hardware configurations can impact the efficiency and outcomes of scientific research.

One case study involves a research group from a well-known university that switched from using older GeForce GPUs to the latest RTX series for their Cryo-EM analyses. They reported a significant reduction in processing time, from several days to just a few hours, without compromising the accuracy of their results. This enhancement in speed allowed them to increase their throughput and take on more complex projects.

Another example comes from a pharmaceutical company that uses high-end Tesla GPUs for drug discovery. Their team emphasized not only the speed but also the reliability of these GPUs, which is crucial in high-stakes research where every minute counts. The Tesla GPUs enabled them to rapidly iterate through molecular models, accelerating the drug development process.

These experiences underline a common theme: the choice of GPU can have a profound impact on the efficiency and scalability of Cryo-EM research. While higher-end GPUs like the Tesla and Quadro series offer the best performance, mid-range GPUs like the RTX series provide a more accessible option for many academic institutions, without a significant compromise in speed or accuracy.

Such real-world examples highlight the tangible benefits of investing in the right GPU workstation, reinforcing the idea that the upfront cost can be outweighed by the gains in research capabilities and efficiency.

The journey through the realms of Cryo-EM and the pivotal role of GPU technology in advancing this field culminates with a clear understanding of the impact and importance of these tools. RELION, empowered by NVIDIA's GPU computing, has not only accelerated the pace of biomolecular research but has also democratized high-level scientific investigations, making them more accessible and efficient.

From the benchmarks and case studies, it's evident that the choice of GPU has a significant impact on the performance of Cryo-EM research. While high-end GPUs like NVIDIA's Tesla and Quadro series offer unparalleled processing power, mid-range GPUs such as the RTX series present a balanced option for a wider range of users. The decision on the right GPU, along with the appropriate CPU and RAM, should be guided by the specific needs and resources of the research project or institution.

Looking forward, the future of GPU acceleration in Cryo-EM is bright and promising. As GPU technology continues to evolve, we can expect further enhancements in speed, efficiency, and capabilities, paving the way for more groundbreaking discoveries in molecular biology and beyond. The ongoing collaboration between technological innovation and scientific research will undoubtedly continue to push the boundaries of what's possible, revealing ever more intricate details of the world at the molecular level.

The integration of GPUs in Cryo-EM research, especially through the use of RELION, signifies a monumental leap in the field of molecular biology. As technology and science continue to evolve in tandem, the importance of selecting the right hardware cannot be overstated. To this end, Bizon Tech offers specialized Cryo-EM workstation computers, tailored to meet the demanding requirements of this advanced research. These workstations are not just about powerful components; they represent a synergy of cutting-edge technology and scientific exploration, enabling researchers to unlock new potentials in Cryo-EM and push the boundaries of molecular discovery. With Bizon Tech, scientists and researchers are equipped with the tools necessary to navigate the complex world of Cryo-EM, paving the way for future breakthroughs and continued innovation in the field.

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