AI in Genomics
- AI in Genomics: Server Configuration
This article details the server configuration required for running Artificial Intelligence (AI) workloads applied to genomic data. It is aimed at system administrators and bioinformaticians new to deploying these systems within our infrastructure. We will cover hardware, software, and key considerations for a successful deployment.
Introduction
The application of AI, particularly Machine Learning and Deep Learning, to genomics is rapidly expanding. Tasks such as Genome Assembly, Variant Calling, Gene Expression Analysis, and Protein Structure Prediction are increasingly relying on computationally intensive algorithms. This necessitates robust and scalable server infrastructure. This document outlines the recommended specifications for building such a system. Understanding Big Data concepts is crucial for managing genomic datasets.
Hardware Requirements
The hardware forms the foundation of any AI-driven genomics pipeline. The following table details the recommended specifications for a base server. These specifications can be scaled up depending on the size and complexity of the datasets and models used. Consider using a Rack Server for optimal density.
| Component | Specification |
|---|---|
| CPU | Dual Intel Xeon Gold 6338 (32 cores per CPU, 64 total) or AMD EPYC 7763 (64 cores) |
| RAM | 512 GB DDR4 ECC Registered RAM (minimum), 1TB recommended |
| Storage (OS & Software) | 1 TB NVMe SSD |
| Storage (Data) | 10 TB+ NVMe SSD RAID 0 or RAID 10 (depending on performance/redundancy needs) or high-performance Network Attached Storage (NAS). Consider Object Storage for very large datasets. |
| GPU | 4 x NVIDIA A100 80GB GPUs or equivalent (e.g. AMD Instinct MI250X) |
| Networking | 100 Gbps Ethernet or Infiniband |
| Power Supply | Redundant 2000W Power Supplies |
Software Stack
The software stack must be carefully chosen to support the AI frameworks and genomic tools. We standardize on a Linux distribution for server deployments. See our Linux Server Setup guide for details.
Operating System
- Ubuntu Server 22.04 LTS (Recommended)
- CentOS Stream 9
AI Frameworks
- TensorFlow 2.x
- PyTorch 1.x
- Keras (integrated with TensorFlow)
Genomic Tools
- BWA (Burrows-Wheeler Aligner)
- SAMtools (Sequence Alignment/Map Tools)
- GATK (Genome Analysis Toolkit)
- VCFtools (Variant Calling Format Tools)
Containerization
- Docker – for packaging and deploying applications.
- Kubernetes – for orchestrating containerized workloads (recommended for large-scale deployments).
Storage Configuration Details
Choosing the right storage solution is critical. Genomic data is often very large and requires high throughput. Here’s a more detailed breakdown of storage considerations:
| Storage Type | Use Case | Capacity | Performance |
|---|---|---|---|
| NVMe SSD (RAID 0) | Active data processing, model training, temporary files | 2-10 TB | Very High (Read/Write) |
| NVMe SSD (RAID 10) | Critical data storage, redundancy | 10+ TB | High (Read/Write) with redundancy |
| Network Attached Storage (NAS) | Long-term data archiving, large datasets | 50+ TB | Moderate to High (depending on NAS configuration) |
| Object Storage (e.g., S3) | Archival, disaster recovery, large-scale data sharing | 100+ TB | Moderate (Read/Write) |
It's recommended to implement a tiered storage approach, leveraging the speed of NVMe SSDs for active workloads and the cost-effectiveness of NAS or Object Storage for long-term archiving. Review the Data Backup Policy before implementation.
Networking Considerations
High-bandwidth, low-latency networking is essential for transferring large genomic datasets between servers and storage systems.
| Network Component | Specification |
|---|---|
| Network Interface Cards (NICs) | Dual 100 Gbps Ethernet or Infiniband |
| Switch | 100 Gbps Ethernet Switch or Infiniband Switch |
| Interconnect | Fiber Optic Cables (OM4 or better) |
| Network Protocol | RDMA over Converged Ethernet (RoCE) for low-latency communication |
Proper network configuration, including VLAN segmentation and quality of service (QoS) settings, is crucial for ensuring optimal performance.
Monitoring and Management
Continuous monitoring and management are vital for maintaining the health and performance of the server infrastructure. Utilize our standard Server Monitoring Tools such as Prometheus and Grafana. Regularly review System Logs to identify and resolve potential issues. Automated alerts should be configured to notify administrators of critical events.
Intel-Based Server Configurations
| Configuration | Specifications | Benchmark |
|---|---|---|
| Core i7-6700K/7700 Server | 64 GB DDR4, NVMe SSD 2 x 512 GB | CPU Benchmark: 8046 |
| Core i7-8700 Server | 64 GB DDR4, NVMe SSD 2x1 TB | CPU Benchmark: 13124 |
| Core i9-9900K Server | 128 GB DDR4, NVMe SSD 2 x 1 TB | CPU Benchmark: 49969 |
| Core i9-13900 Server (64GB) | 64 GB RAM, 2x2 TB NVMe SSD | |
| Core i9-13900 Server (128GB) | 128 GB RAM, 2x2 TB NVMe SSD | |
| Core i5-13500 Server (64GB) | 64 GB RAM, 2x500 GB NVMe SSD | |
| Core i5-13500 Server (128GB) | 128 GB RAM, 2x500 GB NVMe SSD | |
| Core i5-13500 Workstation | 64 GB DDR5 RAM, 2 NVMe SSD, NVIDIA RTX 4000 |
AMD-Based Server Configurations
| Configuration | Specifications | Benchmark |
|---|---|---|
| Ryzen 5 3600 Server | 64 GB RAM, 2x480 GB NVMe | CPU Benchmark: 17849 |
| Ryzen 7 7700 Server | 64 GB DDR5 RAM, 2x1 TB NVMe | CPU Benchmark: 35224 |
| Ryzen 9 5950X Server | 128 GB RAM, 2x4 TB NVMe | CPU Benchmark: 46045 |
| Ryzen 9 7950X Server | 128 GB DDR5 ECC, 2x2 TB NVMe | CPU Benchmark: 63561 |
| EPYC 7502P Server (128GB/1TB) | 128 GB RAM, 1 TB NVMe | CPU Benchmark: 48021 |
| EPYC 7502P Server (128GB/2TB) | 128 GB RAM, 2 TB NVMe | CPU Benchmark: 48021 |
| EPYC 7502P Server (128GB/4TB) | 128 GB RAM, 2x2 TB NVMe | CPU Benchmark: 48021 |
| EPYC 7502P Server (256GB/1TB) | 256 GB RAM, 1 TB NVMe | CPU Benchmark: 48021 |
| EPYC 7502P Server (256GB/4TB) | 256 GB RAM, 2x2 TB NVMe | CPU Benchmark: 48021 |
| EPYC 9454P Server | 256 GB RAM, 2x2 TB NVMe |
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⚠️ *Note: All benchmark scores are approximate and may vary based on configuration. Server availability subject to stock.* ⚠️