High Performance Computing Working Group - 2014 MSM

Working Group leads: Pratul AgarwalYufang Jin

2013 Meeting Material:

Working group activities and plans: File:HPC progress and plans.pdf

Goals and Objectives:

The goal of this working group is to initiate discussion, foster collaboration and data sharing including (but not limited) to:

  1. Computational resources including high performance computing.
  2. Multi-scale modeling and simulations on emerging computer architectures (e.g. GPUs).
  3. Computational algorithms, libraries, tool-kits and software.
  4. Infrastructure and strategies to handle big-data problems.

Participation in Working Group:

Evolved from Working Group 5.

Currently, feed-back is being sought from various members of the community regarding the need and availability of the computing resources.

Please send your responses by e-mail to the working group leads. Single word responses (yes/no) or responses to partial list are fully acceptable.

Topic: Computing Hardware Resources

  1. Some researchers already have access to what they need (computers, university clusters, storage space) but not everybody. Do you need access to computing resources that are not currently available to your multi-scale modeling needs?
  2. At last year meeting, questions was raised at the meeting about access to supercomputers. Would it be beneficial to coordinate access for MSM Consortium to avail group time on various hardware as needed? Particularly resources at the DOE and NSF centers?
  3. GPUs and other non-standard computer hardware is being used to solve the multi-scale problems. Would you benefits (and also willing) share your experiences and code to benefit members who do not have expertise or human resources to develop the code on their own?
  4. Would cloud computing benefit your investigations? Would you like to access cloud environment such Amazon EC2?

Topic: Computational Algorithms

  1. Do you see the benefits of sharing tool-kits, code, data (?) associated with multi-scale modeling on HPC resources? Would you be willing to share your algorithms and code?
  2. Do you have a wish-list of optimized libraries on the HPC environment, which will improve your productivity while using HPC resources? Could you specify which ones?
  3. If someone wants to seek advice on solving computational problem, do you see the benefits of having a group/forum discussion? These could be simple problems such as what compiler or hardware or libraries to use to solve the problems or something more complex.

Topic: Collaborate, define the needs of the community

  1. It is discussed that 20% of all computing time on NSF supercomputers and 10% of time on DOE supercomputers is used by NIH funded PIs. However, each PI has to write separate proposals (peer-reviewed) and only big users are typically able to get access. Would it benefit to coordinate the access to supercomputers, especially for small to medium sized or beginning users?
  2. Do you see the benefit of organizing focused work-shops to discuss and exchange ideas related to HPC for multi-scale modeling? Either through sessions at existing conferences and meetings? Or perhaps organize new workshop?

MSM Meetings

2013 Meeting

Upcoming Presentations

Past Presentations

Life Sciences on High Performance Computing (HPC) Environment

When: 11:00am - 1:30pm (Eastern Time), Feb. 27th, 2013

The workshop will cover the following topics:

  • What distinguishes HPC from desktop computing
  • Desirable skill sets for leveraging HPC resources
  • How to get an account through TACC and XSEDE
  • Touch on the idea of parallel programming
  • Training opportunities Life Sciences software available at TACC
  • Use case examples of HPC in life sciences


This workshop will be webcast live to the IMAG Multiscale Modeling (MSM)Consortium

Hosted by: The MSM High Performance Computing Working Group

To Access Webcast: http://dlat.utsa.edu/Accordent/Static/UTSAxSpecialEvent+MainCampus_BSE/index.htm

Presentation Slides:HPC_and_Life_Sciences_Prepentation_Slides_Feb_27_2013.pdf

Relevant Infrastructure:

How to set up account to use Texas Advanced Computing Center (TACC)

Requesting a New TACC Account:

  • Connect to the TACC User Portal: https://portal.tacc.utexas.edu;
  • Select the "New User?" link (on the right, below the "Login" button);
  • This page, concerning information for new users, will again be displayed for your review. Click the "Continue" button;
  • A page will be displayed containing the TACC Usage Policy. After reading through the TACC Usage Policy, click the "Accept" button in order to agree you will abide by this policy;

Complete all required information and submit the form;

  • A page will be displayed display confirming you have been successful at requesting an account;
  • You should soon receive a confirmation e-mail from TACC at the e-mail address you provided

containing a URL to verify your e-mail address. Click on the link to validate your e-mail address;

  • After you have successfully verified your e-mail address, your account request will be reviewed by the TACC Accounting Coordinator within one business day. You will be notified when the account request process is complete.
  • After successfully creating a TACC account, users may then log into the TACC User Portal to create a project and request an allocation.

How to set up account to use Extreme Science and Engineering Discovery Environment (XSEDE):https://www.xsede.org/using-xsede

In order to get access to XSEDE resources you must create an XSEDE User Portal (XUP) account. The XSEDE User Portal (XUP) is a web-based, single point-of-entry to the XSEDE system https://portal.xsede.org

  • Allocation request submission capability
  • Access to all your XSEDE accounts and allocated resources
  • Up-to-date information on your accounts and and allocation usage
  • Interfaces for data transfers, data collections, and other user tasks and resources
  • Subscriptions to user news & announcements
  • Training class registration and schedule
  • Access to the XSEDE Help Desk and User Forums

Resources available in Texas Advanced Computing Center: http://www.tacc.utexas.edu/resources

Resources available in Extreme Science and Engineering Discovery Environment: https://www.xsede.org/resources/overview


A brief command summary "cheat sheet" at TACC: http://www.tacc.utexas.edu/c/document_library/get_file?uuid=fd68f2f9-a815-43af-acfd-f85fdf9cb91c&groupId=13601

Challenges and Opportunities:

A Request for Information on novel technologies for high performance computation which is open until 5 April.



List of Participants:

  1. Dr. Hong-Wei Sun
  2. Mr. Philip McQueen
  3. Dr. Weiping Chen
  4. Dr. Susan Gregurick
  5. Dr. Salvador Dura-Bernal
  6. Grace Peng
  7. Dr. Alpay Ozcan
  8. Dr. Hiroshi Ashikaga
  9. Ms. Susan Krauss
  10. Prof. Ranjan Srivastava
  11. Mark Shephard
  12. Dr. Julián Candia
  13. Dr. Maciek Swat
  14. Dr. Jared Weis
  15. Prof. Markus J. Buehler
  16. Mr. Liang-Hui Chu
  17. Prof. Michael Saunders
  18. Dr. Jacob Barhak
  19. Ms. Mei Yan Lee
  20. Mr. Yuekai Sun
  21. Dr. Spyros Stamatelos
  22. Ching-Long Lin
  23. Mr. Andrew Dolan
  24. Warren Anderson
  25. Mr. Hirenkumar Makadia
  26. Dr. Lakshmi Kuttippurathu
  27. Dr. Felice Lightstone
  28. Dr. Pratul Agarwal
  29. Dr. Yufang Jin
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