Molecular Dynamics
CryoSPARC 4.6 Release: 2x GPU Speedup & Enhanced UI
September 12, 2024
3 min read
CryoSPARC v4.6 was released on September 10 with a number of impactful updates. The full list is detailed in the changelog: https://cryosparc.com/updates
Over 2x Speedup on GPUs
CryoSPARC redesigned its input-output code architecture that significantly increases optimizations to particle read times, boasting up to 2.1x speedup across refinement and 2.0x speedup in classification jobs.
CryoSPARC benchmarked on the EMPIAR-10853 dataset, a structure with a 2.3M particle size using box size 300. EMPIAR is a protein complex featuring an MRGPRX2-Gq with peptide Cortistatin-14, a protein implicated in mediating itch, neurogenic inflammation, atopic dermatitis, UC, and more.
- Benchmark on Workstation
- AMD Threadripper PRO 5975WX (32 Cores | 4.5GHz boost)
- NVIDIA GeForce RTX 4090 (24GB GDDR6X)
- Benchmark on Server
- AMD EPYC 7F52 (16 Cores | 3.9GHz Boost)
- NVIDIA A100 PCIe Tensor Core GPU (40GB HBM2)
User Interface Updates
CryoSPARC prides their user interface with easy and organized workflows. Improved Tree, card, and table views for jobs are rebuilt, with dramatic speedups to support large projects. UI is up to 10x faster load time for the tree view and nearly instant interactive updates.
CryoSPARC incorporates new Job Groups allow collapsing multiple jobs into a single card in order to organize, maintain legibility, and keep navigation easy for large projects. Job Groups work across all views, and can be made using multi-selection and the right-click menu.
In the traditional job view, CryoSPARC added a job search menu to quickly find and navigate to any particular job in the project.
Inspect Particle Picks can run without user intervention using a new Auto Cluster mode. Particles are clustered and automatically selected based on their NCC and power scores.
Conclusion
We are excited to see the further adoption and optimizations made by the CryoSPARC team. GPUs have already been a staple for imaging and reconstructing cryo-EM data. For update instructions, please see the CryoSPARC Software Updates and Patches guide.
If you plan to build a computing deployment for CryoSPARC cryo-EM either migrating from cloud services or wanting upgraded hardware, Exxact delivers high-performance custom configurable platforms.
We have been serving top research institutions for decades offering top-of-the-line GPUs that can accelerate your workflow or reduce your total cost of ownership. Contact us today if you have any questions about your next CryoSPARC configuration, and we will be happy to help recommend the best system for your budget, workload, and computing goals.
We're Here to Deliver the Tools to Power Your Research
With access to the highest performing hardware, at Exxact, we can offer the platform optimized for your deployment, budget, and desired performance so you can make an impact with your research!
Configure your CryoSPARC System Today
Molecular Dynamics
CryoSPARC 4.6 Release: 2x GPU Speedup & Enhanced UI
September 12, 20243 min read
CryoSPARC v4.6 was released on September 10 with a number of impactful updates. The full list is detailed in the changelog: https://cryosparc.com/updates
Over 2x Speedup on GPUs
CryoSPARC redesigned its input-output code architecture that significantly increases optimizations to particle read times, boasting up to 2.1x speedup across refinement and 2.0x speedup in classification jobs.
CryoSPARC benchmarked on the EMPIAR-10853 dataset, a structure with a 2.3M particle size using box size 300. EMPIAR is a protein complex featuring an MRGPRX2-Gq with peptide Cortistatin-14, a protein implicated in mediating itch, neurogenic inflammation, atopic dermatitis, UC, and more.
- Benchmark on Workstation
- AMD Threadripper PRO 5975WX (32 Cores | 4.5GHz boost)
- NVIDIA GeForce RTX 4090 (24GB GDDR6X)
- Benchmark on Server
- AMD EPYC 7F52 (16 Cores | 3.9GHz Boost)
- NVIDIA A100 PCIe Tensor Core GPU (40GB HBM2)
User Interface Updates
CryoSPARC prides their user interface with easy and organized workflows. Improved Tree, card, and table views for jobs are rebuilt, with dramatic speedups to support large projects. UI is up to 10x faster load time for the tree view and nearly instant interactive updates.
CryoSPARC incorporates new Job Groups allow collapsing multiple jobs into a single card in order to organize, maintain legibility, and keep navigation easy for large projects. Job Groups work across all views, and can be made using multi-selection and the right-click menu.
In the traditional job view, CryoSPARC added a job search menu to quickly find and navigate to any particular job in the project.
Inspect Particle Picks can run without user intervention using a new Auto Cluster mode. Particles are clustered and automatically selected based on their NCC and power scores.
Conclusion
We are excited to see the further adoption and optimizations made by the CryoSPARC team. GPUs have already been a staple for imaging and reconstructing cryo-EM data. For update instructions, please see the CryoSPARC Software Updates and Patches guide.
If you plan to build a computing deployment for CryoSPARC cryo-EM either migrating from cloud services or wanting upgraded hardware, Exxact delivers high-performance custom configurable platforms.
We have been serving top research institutions for decades offering top-of-the-line GPUs that can accelerate your workflow or reduce your total cost of ownership. Contact us today if you have any questions about your next CryoSPARC configuration, and we will be happy to help recommend the best system for your budget, workload, and computing goals.
We're Here to Deliver the Tools to Power Your Research
With access to the highest performing hardware, at Exxact, we can offer the platform optimized for your deployment, budget, and desired performance so you can make an impact with your research!
Configure your CryoSPARC System Today