High-Performance GPU Systems for CryoSPARC
Purpose-built computational platforms for cryogenic electron microscopy (cryo-EM). Accelerate your single-particle analysis pipelines—from motion correction and 2D classification to sub-angstrom 3D refinement—with our massive multi-GPU architectures.
Cryo-EM Software Ecosystem & Deployment Support
Every CryoSPARC workstation ships with OS installed, NVIDIA CUDA toolkits validated, and GPU drivers configured. Our engineers verify solver execution and run benchmark reconstructions before handover.
We Validate Your Cryo-EM Environment
Skip the complex database and CUDA configurations. Kirti Telnet provisions your hardware with validated NVIDIA drivers, MongoDB dependencies, and pre-configured CryoSPARC Master/Worker node setups so you can begin processing micrographs instantly.
Primary Processing Pipeline
End-to-End Single Particle Analysis
Best for: End-to-End Single Particle Analysis
CryoSPARC Live — Real-time on-the-fly reconstruction during microscope data collection
Alternative / Secondary Pipelines
Cross-Validation of Atomic Models
Best for: Cross-Validation of Atomic Models
cisTEM — User-friendly single-particle image processing suite
Visualization & Modeling
Map Fitting & Atomic Model Building
Best for: Map Fitting & Atomic Model Building
Coot — Macromolecular model building into electron density
Phenix — Automated structure refinement and validation
Supported Operating Systems
HPC & Scientific Compliance
Best for: HPC & Scientific Compliance
Rocky Linux — Enterprise-grade RHEL-compatible OS for scientific computing
Enterprise System Matrix — CryoSPARC GPU Systems
CryoSPARC relies on a delicate balance of resources. Fast CPUs prepare the data, massive PCIe Gen 5 NVMe arrays stream the multi-terabyte movies, and multiple high-VRAM GPUs execute the 3D reconstruction. Our systems are balanced to ensure no component starves the pipeline.
All prices are tentative and subject to change based on configuration and component availability. CryoSPARC software licenses are procured separately.
Entry Cryo-EM Node
Small-scale single-particle datasets and introductory cryo-EM preprocessing with GPU-accelerated motion correction.
RAM: 64 GB DDR5
GPU: 1x NVIDIA RTX 4000 Ada Generation
Storage: 1 TB Gen4 NVMe
Starting Price
Advanced Processing Workstation
Mid-throughput cryo-EM datasets, extended 2D classification runs, and ab-initio 3D reconstruction with ECC-validated memory.
RAM: 128 GB DDR5 ECC (4-Channel)
GPU: 1x NVIDIA RTX 4500 Ada 24GB
Storage: 2 TB Gen4 NVMe
Starting Price
CryoSPARC Live Station (Dual-GPU)
Real-time on-the-fly reconstruction during microscope sessions, simultaneous preprocessing and 3D refinement with 8-channel ECC memory bandwidth.
RAM: 256 GB DDR5 ECC (8-Channel)
GPU: 2x NVIDIA RTX 5000 Ada 32GB
Storage: 2 TB Gen5 NVMe + 2TB Scratch
Starting Price
Extreme Reconstruction Rig (Quad-GPU)
Massive particle datasets, large box sizes exceeding 700³, and high-resolution sub-angstrom refinement with quad 48GB GPU acceleration.
RAM: 512 GB DDR5 ECC (8-Channel)
GPU: 4x NVIDIA RTX 6000 Ada 48GB
Storage: 4 TB Enterprise NVMe RAID
Starting Price
Enterprise Cryo-EM Cluster Node
Distributed CryoSPARC Master/Worker cluster deployments, enterprise job scheduling, multi-dataset parametric sweeps, and quad-GPU L40S compute for maximum reconstruction throughput.
RAM: 1 TB DDR5 ECC Reg (12-Channel)
GPU: 4x NVIDIA L40S 48GB
Storage: 7.68 TB Enterprise U.2 NVMe
Starting Price
Engineering Disclaimer: Optimal reconstruction speed in CryoSPARC scales with GPU VRAM and the number of CUDA cores. Multi-GPU setups require CryoSPARC licensing that supports multi-GPU worker nodes.
Architectural Features & Performance
The Multi-GPU Requirement for CryoSPARC Live
To keep up with modern data collection (generating terabytes of movies per day), a single GPU is rarely enough. We recommend 2 to 4 GPUs per system, allowing you to dedicate GPUs to concurrent tasks: one for preprocessing/motion correction, and others for streaming 2D classification and 3D refinement.
Eliminating the Storage I/O Bottleneck
Cryo-EM generates colossal datasets. Reading massive TIFF/MRC movie files directly dictates pipeline speed. Our workstations utilize PCIe Gen 5 NVMe scratch drives configured in RAID, delivering up to 14,000 MB/s sustained read speeds, ensuring the GPUs are never starved waiting for data to load.
GPU VRAM and Box Sizes
The maximum particle box size you can process is strictly limited by your GPU’s VRAM. While 11GB is the bare minimum for modern data, massive macromolecular complexes require substantial memory. We deploy RTX Ada Generation GPUs with 24GB, 32GB, and 48GB of VRAM to comfortably handle box sizes well over 700³ without crashing.
Frequently Asked Questions
How many GPUs do I need for CryoSPARC?
While CryoSPARC can run on a single GPU, a multi-GPU setup is highly recommended. For CryoSPARC Live, utilizing at least 2 to 4 GPUs allows you to process data synchronously with microscope collection—dedicating GPUs to preprocessing, 2D classification, and 3D refinement simultaneously.
Why is SSD Scratch storage so critical for Cryo-EM?
Preprocessing steps (like motion correction) require fast copies of movie data from the disk to the GPU. Standard hard drives (HDDs) or network-attached storage (NAS) will severely bottleneck this process. An ultra-fast NVMe SSD scratch drive is mandatory for optimal throughput.
Do I need a high-end CPU if the GPU does the heavy lifting?
Yes. CryoSPARC requires a CPU with high memory bandwidth (greater than 100 GB/s) to feed data efficiently to the GPUs. We configure AMD Threadripper PRO and EPYC architectures specifically to maximize this CPU-to-GPU data pipeline.
Does Kirti Telnet provide Master/Worker cluster setups?
Absolutely. For larger core facilities, we can architect a distributed environment with a lightweight Master node (managing the database and web app) orchestrating multiple heavy, multi-GPU Worker nodes for maximum throughput.
Request Custom Cryo-EM Architecture
Talk to KTPL’s infrastructure engineers for a workload assessment and GPU-optimised hardware recommendation for your CryoSPARC cryo-EM environment.
Get in Touch Today for Expert Solutions and Support