PNCC Compute on BOREAL allows users to perform image processing on PNCC CPU and GPU resources free of charge. Each General Access proposal is allowed one PNCC Compute seat. The nominated team member applies for access to the "PNCC Compute" Nodes on the PNNL Supercomputer BOREAL with free allocations of 6,000 node hours per project.
Details to note:
- PNCC Compute is not how you access a proposals data collected at PNCC. Instead every listed project participant can download their project's data at any time via Globus. How do I access data via Globus?
- The application to be awarded PNCC Compute access, is separate and different from your proposal requesting microscope access.
- Access to PNCC Compute can extend two months beyond the proposal close date for microscope access.
Application Process:
- Access to the computing resources requires an application with full background check and that can take up to four months or longer for Foreign Nationals. Most US citizens can be approved within one to four months depending on number of applications processing parallel along with nominated user's responsiveness.
- After completion of the background check, nominated users need to complete online Cybersecurity training before the Secure ID token (allowing remote access to the computing resources) is shipped. This step often causes delays.
- Once the nominated user has received their token and password for remote login, the user will need to schedule a PNCC Compute Onboarding session with the PNCC Compute SPOC. They will introduce the BOREAL system, job submission protocols, highlight paths to various cryo-EM software, script templates and confirm the ability to login.
If interested in a PNCC Compute account contact the PNCC User Office for information on how to request access.
Available* software on BOREAL include:
- RELION
- cryoSPARC
- EMAN2
- FREALIGN
- DYNAMO
- IMOD
- EMClarity
- MotionCorr 2
- CTFFind4
- PHENIX
- pyem
- Alphafold2
*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, 1TB SSD, and 256GB memory. All are linked to 3PB parallel filesystems via FDR Infiniband network. Standard priority access to the other normal BOREAL nodes (1380 CPU only nodes) is also provided with the same badging and login.