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Computational Systems

Structural Biology computational resources include systems designed specifically for researchers to collect and process data efficiently.  These resources include HPC clusters, SMP/GPU systems, and workstation-class user systems.

HPC Clusters

  • Vision: Vision consists of 12 compute nodes and head node with 26TB solid-state storage.  It utilizes a clustered and parallelized scalable storage system, currently at 420TB.  Compute nodes each contain AMD EPYC CPU's with at least 512GB RAM.  The compute nodes have high-performance 4TB SSD local scratch space.  Nodes contain up to 6 Nvidia GPUs for CUDA accelerated applications.  Cluster communication is via InfiniBand.  In total there are 448 EPYC CPU cores with 7168GB RAM, and 154,624 CUDA cores.
  • Ultron:  Ultron consists of 12 compute nodes and a head node with solid-state storage.  Compute nodes each have dual 14-core 2.4GHz Intel Xeon E5-2680 CPU’s with 256GB RAM.  All compute nodes have 512GB SSD drives as local scratch space.  20 NVidia Tesla K80 processors are available for CUDA accelerated applications.  Cluster communication is via InfiniBand.  In total there are 320 Xeon CPU cores with 2.8TB of RAM, and 49,920 GPU/CUDA cores with 240GB GDDR5.

GPU/SMP Systems

  • Executor:  This 64 core computer consists of 2 32 Core AMD "Epyc" CPU’s running at a boost clock of up to 3.0GHz.  It has 512GB of fast DDR4 shared memory for processing that needs to utilize large blocks of memory at once.  The machine also has 20TB of high-performance scratch local disk space for ultra-high speed processing of large datasets.  It contains two RTX 2080 TI GPU co-processors for CUDA accelerated applications, giving it a total of 8,704 CUDA cores and 22GB GDDR5.
  • Archer:  This 48 core computer consists of 2 24-core Intel Xeon CPUs and has 256GB of shared memory for processing that needs to utilize large amounts of memory and GPU accelerated resources.  It has two Tesla K40 GPU's for a total of 5760 compute cores running at 875MHz and 24GB of GPU memory.  The machine also has 1TB of ultra-fast solid-state local scratch space.
  • Allspark: This 128 core system provides real-time processing and storage for CryoEM Krios data.

General Resources

  • The Structural Biology computer network consists of over 380 computer systems throughout the department for individual, shared, and instrument use. 
  • We have two computer labs consisting of 19 workstation-class Linux computers with access to data processing and structure analysis programs. Scientific software environments and versioning are managed with environment modules.  These computers and software are available to all of the faculty and students in our department.
  • Network storage is provided using a flexible and dynamically tiered SAN architecture.  The SAN passes data over an independent and redundant 10-gigabit-ethernet backplane.  The SAN combined with direct-attached storage resources currently provide over 1.5 Petabytes of capacity to network users.
  • High Performance Computing systems for structural calculations consist of two symmetric multi-processor systems with GPU capability and two HPC clusters.