High Performance Computing Program

Table of Contents

3/6/17

• High Performance Computing User Group & Office Hours – The HPC Program is developing a user group with the objective of serving those requiring HPC assistance, and expanding the HPC community within the NCI intramural community.  The program will be implementing office hours in Frederick on a recurring basis, to serve as points of interaction among the developing HPC community and to aid those with HPC-specific needs or questions.
• Stay tuned for more information – please contact Eric Stahlberg (eric.stahlberg@nih.gov) or Miles Kimbrough (miles.kimbrough@nih.gov) to discuss further.
• CANDLE Workshop – Serving as one of the key computational frameworks to support the NCI DOE Collaboration, the CANcer Distributed Learning Environment is designed to use machine-learning algorithms to find patterns in large datasets with the goal of offering insights that may ultimately result in improved cancer treatment.  Using this computational architecture, participating DOE labs are focused on accelerating methods to identify promising new treatments; deepening understanding of cancer biology; and understanding the impact of new diagnostics, treatments and patient factors in cancer outcomes.  
• There will be a workshop on April 18-19 at the NIH which will provide an opportunity to learn more about deep learning, share insights into research, and explore the potential through open-ended discussions and hands-on activities.
• Stay tuned for more information and registration details – please contact Miles Kimbrough (miles.kimbrough@nih.gov) or Eric Stahlberg (eric.stahlberg@nih.gov) with questions or to discuss further.
• Globus user-focused Webinar – Globus, a cloud-authenticated data management and transfer platform, will be hosting a user-focused webinar in mid-April to benefit those interested in exchanging datasets across a variety of sources.  The webinar will provide a high-level overview of Globus, steps to start using the service, and common use cases along the following topics:

• • When, where, and why to use Globus?
  • NIH account specs - distinction from Globus Plus
  • What do system administrators need to set up managed endpoints?
  • Which endpoints are already set up?
  • How to set up Globus on your own desktop
  • How to transfer and share data
  • If sharing with collaborator, what info does collaborator need?  What do you need to give to collaborator?
  • New Globus command line interface, allowing users to script their transfers
  • Encryption, verification, and expected data transfer speeds as compared to other resources (e.g. FTP)

• More details are forthcoming – in the meantime please contact Miles Kimbrough (miles.kimbrough@nih.gov) to discuss further.

2/6/17

• HPC Data Management Environment 1.0.0 Release – The HPC data management environment (DME) provides a number of application programming interfaces (APIs) to support common scientific data/metadata management functions across the NCI.  Currently in initial release,  HPC DME archive storage can be a permanent storage solution for user data, and can be used as a platform to search, manage and transfer data onto other storage systems.  Common use scenarios may be characterized as follows:
  • Register a collection (PI Lab, Project, Run, Sample or dataset)
  • Register a single data file/object into storage archive synchronously/asynchronously
  • Perform an update on a metadata attribute
  • Subscribe to a known event
  • Generate a report
  • Update/assign permission
  • Perform simple search functions
  • Download a data file/object to Globus share or local directory
• To obtain an HPC DME account, please contact the DME team at HPC_DME_Admin@nih.gov.  Additional details on the release can be found at https://wiki.nci.nih.gov/display/HPC/HPCS-0006
• For any other questions, please contact either Miles Kimbrough (miles.kimbrough@nih.gov) or Eric Stahlberg (eric.stahlberg@nih.gov)

• 2017 Globus Hackathon – Globus, a cloud-based data management and transfer platform, hosted a Hackathon in January at the NIH main campus to benefit those interested in exchanging datasets across a variety of sources.  The event provided hands-on training, sample code writing, and breakout sessions to the more than 40 attendees.  As the event was very well-received, and due to increasing demand, scheduling efforts are now underway for an NIH-wide user-focused webinar to provide a high-level overview of Globus and steps to start using the service.  More details are forthcoming – in the meantime please contact Miles Kimbrough (miles.kimbrough@nih.gov) to discuss further.

1/10/17

• 2017 Globus Hackathon – Globus, a cloud-based data management and transfer platform, will be hosting a Hackathon at the NIH on January 24-25.  This event will benefit those interested in exchanging datasets across a variety of sources and will be separated into two training sessions based on prior technical experience – a high-level overview for researchers and system administrators, and a developer-focused session.   The Hackathon is free to NIH employees and will include hands-on training, sample code writing, and breakout sessions to promote cross-collaboration.  Register here and review the agenda here.
• CBIIT TechScouts – CBIIT TechScouts currently serves the CBIIT community as an idea-sharing platform which allows members to share new tools, technologies, and methodologies relevant to added workplace efficiency.  In order to promote broader community engagement and increase awareness of this platform, the TechScouts will be undergoing some exciting new developments throughout 2017.  More updates will follow soon – in the meantime, please contact Miles Kimbrough (miles.kimbrough@nih.gov) to discuss further.

12/16/16

• SuperComputing 2016 - As a follow-up to the 2016 International Conference for High Performance Computing, a blog has been made available on the NCIP Hub which summarizes NCI's involvement in the conference and sheds light on the challenges and opportunities that lay ahead.  The blog can be found at https://ncip.nci.nih.gov/blog/precision-medicine-inspires-hpc/.
  
  

12/8/16

• Frontiers of Predictive Oncology and Computing Meeting (FPOC)– With over 100 attendees from across the Department of Energy, the National Cancer Institute, academia, industry and other government agencies, the FPOC meeting (hosted by Intel July 12-14, 2016) provided an opportunity to gain insight into challenges and opportunities for the future. The white paper summarizing the meeting is now available through Intel’s website and can be found at http://www.intel.com/content/www/us/en/government/predictive-oncology-and-computing.html.
• SuperComputing 2016 – The 2016 International Conference for High Performance Computing welcomed NCI CIO, Dr. Warren Kibbe and other representatives from CBIIT in Salt Lake City, UT, November 12-18, for a series of presentations and workshop sessions.  These included a Computational Approaches for Cancer workshop, a Plenary Session with Dr. Kibbe serving as a panelist, and a Birds-of-a-Feather session.  Electronic copies of these presentations will be circulated over the next month – more information on the conference can be found at http://sc16.supercomputing.org/.
• 2017 Globus Hackathon – Globus, a cloud-based data management and transfer platform, will be hosting a Hackathon at the NIH on January 24-25.  The Hackathon is free to NIH employees and will include hands-on training, sample code writing, and breakout sessions to promote cross-collaboration.  Register here and review the agenda here.
• Communications about HPC in NCI – To reflect current and emerging efforts of the NCI’s collaboration with the DOE, a landing page has been created at http://hpc.cancer.gov which will provide an anchor point for new developments and resources related to the collaboration.
• HPC Education and Training – As a part of ongoing outreach efforts, The HPC Program will be coordinating a PI-level presentation with the CCR in early January.  Primary presentation will include application domains, NCI DOE collaborative updates, and Big Data management, among others.  For more information, please contact Eric Stahlberg (eric.stahlberg@nih.gov) or George Zaki (george.zaki@nih.gov). 

10/3/16

• High Performance Computing (HPC) Education & Training – The HPC Program will be sponsoring a Graphics Processing Unit (GPU) Training Workshop on Tuesday, October 25^th, in collaboration with CIT.  The workshop will cover the fundamentals of GPU architecture and programming through hands-on exercises.  Please contact either George Zaki (George.zaki@nih.gov) or Miles Kimbrough (miles.kimbrough@nih.gov) for more information.
• 2017 Globus Hackathon – Globus, a cloud-based data management and exchange platform, will be hosting a Hackathon at the NCI in late January.  The Hackathon will include hands-on training, sample code writing, and breakout sessions to promote cross-collaboration.  Stay tuned for further information and registration details.
• HPC and Data Management Support – For assistance with Globus, GPUs, and other high-performance computing or data management needs, visit NCI at Your Service (service.cancer.gov) and simply submit a request for support using the ‘High Performance Computing / Data Management’ request button. Or, simply email George Zaki (george.zaki@nih.gov) or Miles Kimbrough (miles.kimbrough@nih.gov) to get started. 

9/6/16

• Archive Data Management – A new archive data service for large data is now available for evaluation. The new service provides application interfaces to readily access backend storage technologies such as the new Cleversafe storage moved into production last month. Individuals and groups interested in learning more about how this resource may benefit current initiatives may reach out and contact Eric Stahlberg, Miles Kimbrough or George Zaki. 
• Education and Training -  Learn more about how high-performance computing (HPC) can be used to accelerate cancer research and clinical applications. Individuals and groups interested in learning more about HPC, either in general or with specific technologies and scientific challenges in mind may reach out and contact Eric Stahlberg, Miles Kimbrough or George Zaki.
• The upcoming Computational Approaches for Cancer workshop scheduled for November 13, 2016 as part of the International Conference for High Performance Computing, Networking, Storage and Analysis has extended a call for extended abstracts until September 15, 2016. More information can be obtained at the link http://www.scworkshops.net/cancer2016/.
  
  

8/8/16

• Frontiers of Predictive Oncology and Computing Meeting - With over 100 attendees from across the Department of Energy, NCI, academia, industry and other government agencies, the meeting (hosted by Intel July 12-14, 2016) provided an opportunity to gain insight into challenges and opportunities for the future. A white paper summarizing the meeting is to be developed.
• New Data Services with Cleversafe – The Cleversafe storage system officially was moved into a production operational status at the beginning of August. Led by the IT Operations Group at Frederick National Laboratory and working with many stakeholders including CCR, CBIIT and NIH CIT, the new system is used within industry and in key efforts such as the Genomic Data Commons to provide a high level of data assurance for archive and stable data. Stay tuned for further information on opportunities to learn more how this new resource may benefit your scientific and operational needs.
• Education and Training - Plans are underway to develop educational opportunities to learn more about how high-performance computing (HPC) can be used to accelerate cancer research and clinical applications. Individuals and groups interested in learning more about HPC, either in general or with specific technologies and scientific challenges in mind may reach out and contact Eric Stahlberg, Miles Kimbrough or George Zaki.
• Computational Approaches for Cancer workshop - Scheduled for November 13, 2016 as part of the International Conference for High Performance Computing, Networking, Storage and Analysis. A call for papers has been issued. More information can be obtained at the link http://www.scworkshops.net/cancer2016/