EMSL: Capabilities - MSCF CGCA Call for Proposals

Guidelines and Criteria for Submitting a Computational Grand-Challenge Application in Environmental Molecular Science Research

Overview

The Molecular Science Computing Facility (MSCF) is soliciting proposals for allocations of computer time for Computational Grand-Challenge Applications (CGCA) of up to three years duration in environmental molecular science basic and applied research areas that address the environmental problems and research needs facing the U.S. Department of Energy (DOE) and the Nation. Current research projects being carried out at the MSCF are described in the EMSL Research Areas overview. Some potential environmental molecular science proposal topics are listed below.

(bio)geochemistry (e.g. bioremediation and interactions at mineral interfaces)
chemistry of actinides and heavy element systems in the environment
accurate properties of contaminants and waste forms
chemical or physical separations agents for mixed wastes
reactions in solution (e.g., fate and transport of chemical wastes, aqueous structure of metal ions)
interactions at interfaces
biological interactions (e.g. protein structure and behavior, weak interactions, and electronic effects)
thermochemistry and kinetics of environmentally relevant systems (e.g., "green" processing technologies)
reactive transport in subsurface environments
atmospheric (aerosol) chemistry
computational biology (e.g. multiscale modeling of biological processes)

EMSL Science Themes represent EMSL's focus areas, and provide insight to the kinds of projects being solicited. The MSCF "Greenbook" (.pdf, 2.37Mb), describing the science drivers for the procurement of the next-generation high performance computer provides additional directions.

Facility

The MSCF is a high performance computing facility located in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). The EMSL is funded by the Office of Biological and Environmental Research (OBER) in the U.S. Department of Energy.

The MSCF production computing resources for the fiscal year 2009 are comprised of:

HP/Linux 163 TFlops Peak Theoretical Performance
- 2,310 Node/4,620 AMD Quad-core processors
- 36.96 Terabytes of memory (RAM)
- 1.33 Petabytes of local scratch disk
- 250 Terabyte shared cluster file system
740-Terabyte high performance disk archive storage
Molecular Science Software Suite (MS3)
Graphics and visualization laboratory

Scientific consultants are available to help MSCF users access the facility and make efficient use of its resources. We anticipate a next-generation computational resource will become available within the three year scope of projects awarded time as part of this call. New MSCF hardware and software will be made available to the CGCA once it is production ready.

Computational Grand-Challenge Projects

To obtain optimal impact of the MSCF computational resources in addressing the DOE's critical environmental problems, only a few large proposals will be awarded computer time allocations on MSCF resources. This approach is based on the "Grand Challenge Applications" concept used successfully by EMSL and the Mathematical, Information, and Computational Sciences (MICS) Division within the Office of Advanced Scientific Computing Research (ASCR) of DOE. Grand-Challenges are complex, large-scale problems in science and engineering with broad scientific and environmental or economic impacts whose solution can be advanced by applying high-performance computing techniques and resources. The use of teams of scientists with different backgrounds and capabilities provides the largest scientific impact for solving the complex environmental and scientific problems facing the DOE and the Nation. Such teams also enable the training of students and postdoctoral fellows in the use of high performance computing to tackle complex problems. The idea of teams of researchers undertaking such large computational problems is also consistent with the basic tenets of the EMSL, which is a collaborative national user facility.

Guidelines

Computational Grand-Challenge Applications are expected to utilize the MSCF resources predominantly for large-scale parallel calculations that scale efficiently with both the number of processors and size of problem. On the current system, CGCA calculations typically utilize from 32 to 512 nodes (256 to 4096 cores). It is recognized and allowable that projects may periodically need to run calculations with less than 32 nodes as part of a proof-of-concept or software development activity. This type activity will be allowed but it is expected that they will be a minor component of each proposal. We encourage applications that require more than 512 nodes.

Project proposals are expected to comprise multiple investigators working collaboratively as a team. A collaborative team approach provides an excellent mechanism to engage the expertise of researchers from a variety of institutions to be focused on the basic and applied research projects needed to solve the DOE's and the Nation's environmental problems. Teams should consist of computational scientists from universities, national laboratories, and, where appropriate, industry. The teams should be balanced in such a manner to make the most effective use of the MSCF resources in accomplishing their proposed CGCA objectives.

Projects will have a Team Leader. The Team Leader will have the responsibility to make certain that the allocated MSCF resources are utilized in an optimal way and the efforts of the team remain focused on the proposed research project. The Team Leader will also be responsible for reports and reviews of the team's research progress and accomplishments and for managing the allocation of computer resources to team members. Team Leaders will work with MSCF management to optimize overall effectiveness and use of MSCF resources. Changes in the Team Leader will need the approval of MSCF management for continuing time allocations, and may require peer review if the change is viewed to be a substantive change in direction for the CGCA.

CGCA proposals usually are for three years. MSCF resource allocations will be made to projects on a yearly (fiscal year, October through September) basis. Continuation of a CGCA allocation over the 3-year period will be determined based on evidence presented in their Annual Reports and yearly reviews. Appropriate progress must be made relative to that of other projects and/or proposals and the work done needs to be consistent with the proposed work. Continuation after three years will require submission of a new CGCA. For additional details, see Awards section below.

Coupling experiment with theory, modeling or simulation is strongly encouraged and such applications will be preferred over those that do not have an experimental component.

Submission and Selection Dates

The following dates should be noted. Letters-of-Intent may be sent any time between April 1st and May 15th but do not submit a full CGCA proposal until you are requested to do so.

May 15, 2008: Letter-of-Intent due.
June 30, 2008 5:00PM PST: CGCA proposals due.
September 15, 2008: Accepted CGCA proposals announced.
October 1, 2008: Allocated time begins

Letter-of-Intent Submission

The Letter-of-Intent should be submitted by May 15^th by the Principal Investigator (PI) as an indication that a full proposal will be submitted. The Letter-of-Intent will be used to determine whether the proposed research fits within the EMSL mission and to define a list of potential reviewers. The Letter-of-Intent should be submitted to mscf@emsl.pnl.gov and include the following:

Research title,
Extended Abstract (1000 Words) discussing the proposed scientific research relative to the EMSL mission, method and/or approach, and software to be used or developed,
Team list with complete affiliation including institution and position,
Total estimated computing allocation needs,
List of 3 to 5 potential reviewers with complete affiliation, address and phone number.

If the Letter-of-Intent is complete and fits within the criteria mentioned above, the PI will be encouraged to submit a full proposal within a week of receiving the Letter-of-Intent. The complete proposal must be submitted via the EMSL User System (see Proposal Submission section).

Proposal Submission

The Team Leader (PI) is required to submit the CGCA proposal for their team. All proposals are required to be submitted electronically. No paper proposals will be accepted. All parts of the proposal form must be completed and submitted together at the same time for a proposal to be considered complete. Incomplete proposals will not be accepted or reviewed. All proposals must follow the instructions and format specified in the MSCF CGCA Proposal Guide (PDF or Microsoft Word). Proposals that do not follow the instructions, omit required information, or deviate from the proposal format will be considered as incomplete proposals, and will not be accepted or reviewed.

The complete proposal must be submitted via the EMSL Usage Portal (the user interface to the EMSL Usage System, EUS). Part of the EUS requires details about team members and affiliations and are listed in the Proposal Guide. Large text sections can be attached as Microsoft Word files or Adobe PDF files. Once a proposal is submitted, the PI can no longer make changes, however, a read-only copy is available via the EMSL Usage Portal..

Questions about submission of the MSCF CGCA Proposal or changes that need to be made should be directed to the MSCF Contact (see Additional Information section below).

An acknowledgment for receipt of a complete proposal will be sent by e-mail to the Team Leader (PI).

Proposal Evaluation and Selection

We seek applications of Grand-Challenge molecular science research that require large numbers of processors and a significant portion of our computational resources. Proposals will be reviewed and selected based upon the following criteria.

scientific merit
appropriateness of the proposed method or approach
relevance to the EMSL science themes and research needs of the DOE and the Nation
potential to contribute significantly to highly cited publications
reasonableness and appropriateness of the proposed computer resources

All complete proposals will be reviewed by external scientific peer reviewers. Scientific peer reviewers will be chosen with regard to both their scientific expertise and the absence of conflict-of-interest issues. The project proposals selected for allocation awards will be reviewed internally before final approval.

Awards

It is expected that only 5 or 6 CGC proposals will receive allocation awards in this round of proposals. Computer resource allocations on the MSCF production computers will be made to selected projects for a one-year period, contingent upon the availability of resources (expected to be 8 million node-hours for FY09). Allocation award sizes are expected to be on the order of 350,000-2,000,000 node-hours for a one-year period, each node having 8 cores available. Allocations for the second and third year of the project are contingent upon the progress-to-date, accomplishments, and projected needs of the project relative to that of other projects and/or proposals. Only allocations of time on MSCF production computer resources will be awarded. No awards of funding for salaries, travel, equipment, or supplies will be made. The MSCF reserves the right to award allocations in whole or in part to any or none of the proposals received in response to this notice.

All awarded proposals are subject to both the Use Policy for research done in the EMSL and the Support and User Policies for the MSCF.

Publication of Awards

CGCA proposals that are selected and awarded allocations will have the following information published electronically on the web and possibly in press materials or reports to sponsoring agencies.

Title
Team leader and institution
Team members and institutions
Proposal abstract
Resource allocation for current year
Research highlights

Team Leaders (PI) will be responsible for periodically providing highlights, publications, recognitions and awards that are a result of the research activities. Information on the previous projects selected for awards in prior MSCF calls for proposals is available.

Additional Information

For additional information or questions contact:

Erich R. Vorpagel, Ph.D.
Manager Computational Grand-Challenge and Other Projects
MSCF Visualization & User Services
William R. Wiley Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
P.O. Box 999, MS K8-83
Richland, WA 99352
telephone: (509) 371-6448
facsimile: (509) 371-6110
E-mail: erich.vorpagel@emsl.pnl.gov

Questions should be submitted to mscf@emsl.pnl.gov.