What is PNCC Compute?

PNCC Compute Explained

  • All data collected at PNCC is available to users in two formats – raw data and pre-processed (Motion Corrected and CTF Fit). For instructions to download the data see the FAQs page. 
  • In addition to downloading the data, General Access Proposals can have one team member request access to the PNCC Compute Nodes on the EMSL Supercomputer CASCADE with free allocations of 2,000 node hours per project.
  • The process for access to the computing resources requires a background check and can take a month or longer for Foreign Nationals. Most US citizens can be approved in less than a month. 
  • Contact the PNCC User Coordinator for information on how to request access to PNCC Compute on CASCADE. Once access is approved, you receive your Secure ID token. Then will schedule an onboarding session with our PNCC Computing SPOC to introduce you to the CASCADE system and job submission protocols. We will, highlight paths to various cryo-EM software and script templates and confirm your ability to login.

Available software on CASCADE include:

  • RELION (1, 2 & 3)
  • CisTEM
  • EMAN2
  • FREALIGN
  • DYNAMO
  • IMOD
  • EMClarity
  • MotionCorr 2
  • CTFFind4
  • PHENIX

Note that other software can be installed on request.

The PNCC Compute Partition provides priority job staging for PNCC projects and consists of fifty-six nodes where each node has 2x 16GB V100 GPGPU, 16 Intel XEON CPU cores, 1 TB SSD, and 256GB memory. All are linked to 3PB parallel filesystem via FDR Infiniband network. Standard priority access to the other normal CASCADE nodes (1380 CPU only nodes) is also provided with the same badging and login.

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