Blog/Article
How bare metal servers are revolutionizing scientific research
March 26, 2025
Scientific computing demands have grown exponentially, with modern projects now processing petabytes of data daily. Traditional virtual machines couldn't possibly handle that efficiently, which is why bare metal servers are the ideal infrastructure solution.
These dedicated servers (another term for bare metal servers) deliver superior performance for data-intensive tasks such as genomic sequencing, climate modeling, and particle physics simulations.
As a result, research institutions worldwide are witnessing dramatic improvements in processing speeds and resource efficiency.
Summary
By the end of this article, you will better understand why scientists can benefit from bare metal infrastructure, exploring performance benefits, cost implications, and the impact on research reproducibility.
The Computational Demands of Modern Scientific Research
Modern scientific research has become increasingly dependent on computational power to process unprecedented volumes of data. In recent years, the explosive growth in scientific data has fundamentally transformed how research is conducted across disciplines.
Data Explosion in Scientific Fields
The scientific community is experiencing a data deluge that shows no signs of slowing down. For example, more than one million papers are added annually to the PubMed index in the biomedical field alone.
This massive influx of information creates what researchers call a "poverty of attention" despite the wealth of available data. Scientists often face severe limitations in finding, assimilating, and manipulating this information.
Processing Requirements for Complex Simulations
Complex simulations represent one of modern scientific inquiry's most computationally demanding aspects. These simulations require substantial processing power to solve intricate mathematical models that capture physical phenomena.
Scientific applications particularly demanding of computational resources may include:
Fluid dynamics and plasma simulations: Requiring resolution of equations across multiple spatial scales and time steps.
Genomic sequencing: Processing terabytes of genetic data.
Climate modeling: Simulating complex environmental systems with countless variables.
Particle physics: Modeling subatomic interactions at unprecedented scales.
For many of these applications, traditional computing approaches fall short. Scientists face a dilemma wherein the complexity of their models often exceeds available computing resources.
Due to this limitation, researchers frequently spend considerable time "defeaturing" models—removing details to reduce computational demands—which can compromise accuracy.
Additionally, the computational requirements for simulating transient and turbulent problems, exploring fatigue, analyzing nonlinearities, and generating thousands of design variations typically exceed what standard workstations can provide.
Why Virtual Machines Fall Short for Scientific Computing
Despite widespread adoption in enterprise computing, virtual machines present significant limitations for scientific workloads.
The primary drawback stems from their architecture—VMs introduce a virtualization layer between the operating system and hardware, creating meaningful performance overhead.
Time measurements in virtual machines may exhibit varying degrees of accuracy depending on the hypervisor implementation. While modern hypervisors have improved timer virtualization, high-precision timing operations can still show discrepancies in specific scenarios.
This limitation is particularly relevant for runtime comparisons of algorithms and other performance-sensitive scientific applications.
Consequently, the growing complexity of scientific simulations combined with these virtualization limitations has driven researchers toward bare metal cloud computing.
Direct hardware access eliminates these bottlenecks while maintaining the cloud infrastructure's flexibility and scalability benefits.
How Bare Metal Architecture Accelerates Scientific Discovery
Bare metal architecture, be it on-prem or through managed hosting, represents a paradigm shift in how scientific workloads access computing resources.
Unlike virtualized environments, this approach provides researchers unfettered access to computational power, memory, and storage—critical factors for data-intensive scientific applications.
Direct Hardware Access: Eliminating the Hypervisor Layer
When operating on bare metal servers, scientific applications gain several key advantages:
Zero abstraction penalties: Applications interact directly with hardware, reducing translation delays that are commonly found in virtualized environments
Complete hardware utilization: All CPU cycles, memory bandwidth, and I/O operations are available to scientific workloads
Consistent performance: No resource contention with other virtual machines sharing the same hardware
Specialized hardware access: Direct utilization of GPUs, FPGAs, and other accelerators essential for scientific computation
Moreover, bare metal servers usually enable scientists to fine-tune hardware configurations for their unique computational requirements.
This customization flexibility proves invaluable for workloads like particle physics simulations or computational chemistry, where even minor improvements in processing efficiency translate to substantial time savings.
Genomic Sequencing Speed Improvements
Perhaps the impact of bare metal architecture is more evident in genomic sequencing, a field where computational efficiency directly correlates with the pace of scientific discovery.
A collaborative study between Illumina, Microsoft Azure, and Pure Storage highlighted remarkable improvements when utilizing a hybrid bare metal/public cloud infrastructure.
Accelerated Data Transfer:
The study revealed that employing array-level replication with Pure Storage's FlashBlade technology enabled the transfer of genomic sample files to cloud environments 35 times faster than traditional FTP methods.
Specifically, moving reference and input files for a 32GB genome sample took merely 2.4 minutes using this optimized infrastructure, compared to 90 minutes per sample with conventional methods.
Enhanced Parallel Processing:
The infrastructure facilitated remarkable parallelization capabilities, allowing the research team to complete secondary analysis on 50 genomic samples (32GB each) in just 60 minutes through parallel processing.
Notably, system latency remained consistently low at 3.6 milliseconds, even when running 50 virtual machines simultaneously, demonstrating exceptional scalability. So, these performance improvements directly translate to scientific advancements.
By processing genomic data 35 times faster, researchers can analyze more samples, test additional hypotheses, and ultimately accelerate the pace of discovery—a clear demonstration of how hybrid cloud architecture with cloud-adjacent storage is transforming scientific research capabilities.
Climate Modeling and Weather Prediction
Weather forecasting and climate research generate massive amounts of environmental data demanding intensive processing capabilities.
Advanced computing with a proven bare metal infrastructure delivers predictive analysis when time is critical, especially since delayed data processing may have catastrophic effects.
Climate modeling requires expert preparation of complex processing jobs with simulations running over varying periods.
Weather centers process data from multiple sources, including satellites, aircraft, radiosondes, ships, and ocean-based buoys, creating unprecedented increases in relevant datasets.
This information must be accurately overlaid upon three-dimensional Earth topography, introducing additional computational complexity.
Global climate modeling involves interconnected data points from winds, temperatures, radiation, gas emissions, cloud formation, land and sea-based ice, vegetation, and numerous other elements.
Bare metal servers equipped with powerful processors and substantial memory make these complex simulations possible, enabling researchers to run calculations that aid in environmental prediction more efficiently than in virtualized environments.
Particle Physics Simulations at CERN
The Large Hadron Collider (LHC) at CERN generates vast amounts of data from particle collision events, necessitating substantial computational resources for effective processing and analysis.
CERN operates an OpenStack-based cloud infrastructure comprising over 300,000 CPU cores to manage this workload. This infrastructure supports the daily execution of hundreds of thousands of physics-related computational tasks.
Data Generation and Processing
Collision Data: The LHC produces millions of particle collisions per second, resulting in significant data that must be processed and analyzed to further our understanding of fundamental physics.
Data Reduction: Given the immense volume of raw data, CERN employs advanced data reduction techniques to filter and retain only the most pertinent information for detailed analysis.
Computational Infrastructure
OpenStack Deployment: CERN utilizes OpenStack to manage its cloud infrastructure, enabling efficient provisioning and management of computational resources.
Bare Metal Provisioning: By integrating OpenStack's Ironic component, CERN provisions physical servers (bare metal) for workloads that demand high performance and low latency.
Physics Simulations
Role in Research: CERN simulations provide theoretical models that are compared against experimental data from the LHC. This comparison is crucial for identifying discrepancies indicating new physics phenomena or refining existing models.
Computational Demands: These simulations involve complex calculations to explore the quantum behaviors contributing to each event, requiring extensive computational power.
In summary, CERN's integration of advanced computing infrastructures, including virtualized environments and bare metal servers, is essential for managing the extensive data and complex simulations inherent in particle physics research.
Computational Chemistry and Drug Discovery
Computational chemistry utilizes computer modeling and simulation to solve complex chemical problems.
Chemists employ bare metal infrastructure for tasks like identifying protein binding sites for drug molecules, modeling synthesis reactions, and exploring physical processes underlying phenomena such as superconductivity or energy storage.
In essence, bare metal servers allow scientists to optimize drug development by focusing on compounds with higher chances of success, thereby reducing costs and time.
Machine learning algorithms trained on these systems can predict drug properties using databases of known compounds, helping identify promising candidates without exhaustive physical testing.
Molecular docking simulations performed on bare metal infrastructure predict the preferred orientation of drug molecules when bound to target proteins with significantly greater speed and accuracy than in virtualized environments.
This capability proves especially valuable for molecular dynamics simulations requiring precise execution over extended periods.
Beyond this, bare metal cloud computing enables high-throughput density functional theory calculations that predict binding energies between drug molecules and their target proteins.
These computations typically overwhelm traditional virtualized environments but thrive on dedicated bare metal servers.
Eliminating Performance Variability in Experiments
Traditional virtualized environments can introduce significant performance variability due to resource contention, commonly known as the "noisy neighbor" effect.
This phenomenon occurs when multiple virtual machines (VMs) share the same physical host, and one or more VMs consume excessive resources, degrading others' performance.
Such resource contention can cause performance degradation, impacting the predictability and reliability of computational tasks.
Bare metal servers, which run applications directly on physical hardware without a hypervisor layer, can mitigate this issue by providing dedicated resources, ensuring consistent performance without interference from other VMs.
The counting method employed can cause variability in results in cell counting experiments. Manual cell counting often has significant variations, leading to data inconsistency between experimental setups and impacting the reproducibility of research.
Automated cell counting methods have been developed to reduce this variability and improve accuracy. Studies have shown that automated counting methods exhibit lower variation coefficients than manual methods, indicating more consistent and reliable results.
Implementing standardized protocols on dedicated hardware, such as bare metal servers, can further enhance the consistency and reliability of experimental outcomes by eliminating performance variability associated with virtualized environments.
Long-term Data Preservation Strategies
Long-term preservation of scientific data faces numerous challenges. The recommended approach follows the industry-standard "3-2-1 rule", used in both bare metal and virtualized environments:
Maintain three copies of important data
Store on two different storage media
Keep at least one copy in the cloud or off-site
Dedicated bare metal storage solutions offer superior options for preserving research data, with cold storage systems ensuring data viability for periods exceeding five years.
These systems provide computational environment documentation that captures operating systems, software versions, and configuration details—essential for future reproducibility.
Cost-Efficiency Analysis for Research Grants and Budgets
Financial constraints often dictate technological decisions in research environments, making cost efficiency crucial when allocating limited grant funding.
Researchers increasingly discover that bare metal cloud computing offers compelling economic advantages alongside performance benefits.
Optimizing Computing Resources for Limited Research Funding
IT administrators face mounting pressure throughout scientific institutions to optimize resource allocation from finite research budgets. Studies show universities can achieve up to 50% savings in infrastructure budgets by centralizing computing resources.
Essentially, scientific computing requires balancing peak demand capabilities with everyday usage patterns.
Case Study: How University Research Clusters Save with Bare Metal
NC State University's Virtual Computing Laboratory (VCL) provides compelling evidence for bare metal efficiency in academic settings. Their cloud computing system delivers educational IT support and research capabilities on shared infrastructure.
The VCL supports over 160,000 non-HPC reservations and 7 million CPU hours annually, with annual costs of approximately USD 2 million.
This delivers a remarkable cost-per-CPU-hour of USD 0.26 to USD 0.27. By integrating teaching and research functions on shared bare metal infrastructure, the university maximizes return on capital investment while minimizing underutilization periods.
NC State's case demonstrates that the academic calendar's cyclical demand patterns can be effectively balanced by allowing HPC research workloads to utilize capacity during educational downtime periods.
This approach enables institutions to achieve both economic efficiency and computational performance needed for scientific advancement.
How Latitude.sh Customers Save Costs and Improve Performance
It's clear by now that bare metal servers have proven to deliver substantial cost savings for various initiatives by providing dedicated, high-performance infrastructure tailored to specific workload requirements.
Latitude.sh, of course, has even more real-world examples to bring to the table.
Neon Labs, a blockchain innovator, migrated from AWS to Latitude.sh's blockchain-optimized bare metal servers and achieved a remarkable 60% reduction in cloud costs while tripling their workload performance.
This transition not only lowered expenses but also significantly enhanced operational efficiency.
Similarly, eOracle experienced substantial savings by adopting Latitude.sh's bare metal servers.
The shift resulted in a threefold reduction in compute costs, enabling eOracle to access greater computing power and faster NVMe drives than their previous virtual machine setup. This change facilitated better performance while maintaining cost-effectiveness.
BTCS, a Web3 company, doubled its infrastructure performance while saving an estimated 30% on cloud costs after transitioning to Latitude.sh's bare metal servers.
This improvement highlights the efficiency of bare metal solutions in delivering high performance at reduced costs.
MUBI leveraged Latitude.sh's bare metal servers in video streaming to enhance streaming quality and reduce infrastructure expenses.
The deployment led to a 35% reduction in infrastructure costs in Brazil, alongside significant improvements in streaming performance, demonstrating the economic and operational benefits of bare metal infrastructure.
These case studies underscore the financial advantages of adopting bare metal servers. By eliminating virtualization overheads and providing dedicated resources, bare metal solutions enable companies to optimize performance while achieving substantial cost reductions.
This approach mainly benefits businesses with high-performance demands, such as blockchain operations and media streaming services.
You Know The Conclusion
Bare metal cloud computing stands as a transformative force in scientific research, offering substantial advantages over traditional virtual machines.
Scientists worldwide report dramatic improvements through direct hardware access, eliminating virtualization overhead that previously constrained their work.
These performance gains, combined with enhanced reproducibility and cost savings, position bare metal cloud computing as an essential platform for modern scientific discovery.
Scientists now process more data, run complex simulations, and accelerate breakthroughs across disciplines, marking a significant advancement in research capabilities.
Bare metal can also benefit you, and the first step is quite simple: create an account with Latitude.sh today!