Plant Phenotyping
- Plant Phenotyping Server Configuration
This document details the recommended server configuration for running plant phenotyping software and associated data processing pipelines. This guide is intended for newcomers to the server administration aspects of our research environment. This setup balances performance, scalability, and data integrity. It assumes a baseline familiarity with Linux server administration and network concepts. Please consult with the System Administrators Group for any questions or concerns.
Overview
Plant phenotyping generates large volumes of data, including images, time-series measurements, and environmental data. A robust server infrastructure is critical for efficient data storage, processing, and analysis. This configuration focuses on a multi-tier architecture: data acquisition, data storage, and processing/analysis. We will primarily focus on the processing/analysis tier, assuming data acquisition servers are handled separately (see Data Acquisition Protocols). Data storage is covered in Data Storage Solutions. This document details the specifications for the processing server.
Server Hardware Specifications
The following table details the minimum and recommended hardware specifications for the plant phenotyping processing server. These specifications are designed to handle typical workloads, but may need adjustment based on specific project requirements. Consider Scalability Considerations when planning future upgrades.
| Component | Minimum Specification | Recommended Specification |
|---|---|---|
| CPU | Intel Xeon E5-2620 v4 (6 cores, 12 threads) | Intel Xeon Gold 6248R (24 cores, 48 threads) |
| RAM | 64 GB DDR4 ECC Registered | 128 GB DDR4 ECC Registered |
| Storage (OS & Software) | 500 GB SSD | 1 TB NVMe SSD |
| Storage (Data Processing) | 4 TB HDD (RAID 1) | 8 TB HDD (RAID 5 or 10) |
| GPU | NVIDIA GeForce RTX 3060 (12 GB VRAM) | NVIDIA RTX A5000 (24 GB VRAM) |
| Network Interface | 1 Gbps Ethernet | 10 Gbps Ethernet |
Software Stack
The following software stack is recommended for the plant phenotyping processing server.
- Operating System: Ubuntu Server 22.04 LTS – Offers excellent stability, security updates, and package availability.
- Programming Languages: Python 3.9 or higher, R 4.2 or higher.
- Data Analysis Libraries: NumPy, SciPy, Pandas, Scikit-learn, OpenCV. These are typically managed using Anaconda.
- Database: PostgreSQL 14 – For storing metadata and analysis results.
- Workflow Management: Nextflow or Snakemake – For automating and managing complex processing pipelines.
- Version Control: Git – For managing code and configuration files. Repository hosted on GitLab.
- Containerization: Docker and Docker Compose – For creating reproducible environments.
Network Configuration
Proper network configuration is crucial for data access and communication. The server should have a static IP address and be accessible via SSH. Firewall rules should be configured to allow only necessary traffic. Refer to the Network Security Policy for detailed guidelines.
| Setting | Value |
|---|---|
| IP Address | Static, assigned by Network Administration |
| Subnet Mask | 255.255.255.0 (example) |
| Gateway | Assigned by Network Administration |
| DNS Servers | 8.8.8.8, 8.8.4.4 (Google Public DNS) |
| SSH Access | Enabled, restricted to authorized users |
| Firewall | UFW (Uncomplicated Firewall) enabled with appropriate rules |
Data Processing Pipeline Configuration
The data processing pipeline is the core of the plant phenotyping workflow. It typically involves image processing, feature extraction, and statistical analysis. Pipelines should be designed to be modular and reproducible. Consider using workflow management systems like Nextflow or Snakemake to orchestrate the pipeline steps. Detailed documentation on pipeline development can be found on the Pipeline Development Wiki.
| Pipeline Stage | Description | Software/Libraries |
|---|---|---|
| Image Preprocessing | Noise reduction, contrast enhancement, and image registration. | OpenCV, Scikit-image |
| Feature Extraction | Identification and measurement of plant traits (e.g., height, area, color). | OpenCV, PlantCV, custom Python scripts |
| Data Analysis | Statistical analysis of extracted features. | R, Pandas, SciPy, Scikit-learn |
| Data Visualization | Creation of charts and graphs to visualize results. | Matplotlib, Seaborn, R ggplot2 |
Security Considerations
Server security is paramount. Regularly update the operating system and software packages. Implement strong passwords and multi-factor authentication. Monitor system logs for suspicious activity. Consult the Security Best Practices document for detailed security guidelines. Data backups should be performed regularly and stored in a secure location (see Backup and Recovery Procedures).
Further Resources
- System Administration Documentation
- Troubleshooting Guide
- Contacting Support
- Data Storage Solutions
- Data Acquisition Protocols
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.* ⚠️