Molecular Science Computing Facility: About MSCF

Previous Highlights

SuperComputing 2003

11/21/03 - Abstract and pictures of the PNNL exhibit at the SuperComputing Conference in Phoenix, Arizona, November 15-21

Scientific Discovery through Advanced Computing

08/14/01 - The Department of Energy today announced its first awards under the new Scientific Discovery through Advanced Computing (SciDAC) program. For more details, see the Office of Science Announcement.

SuperComputing 2000

Abstract, 3D modeled pictures, and a virtual tour of the PNNL exhibit at the 2000 SuperComputing Conference in Dallas, Texas, November 4-10

MSCF Web Site Wins Crystal Award of Distinction in Two Categories

03/29/00 - The MSCF Web Site won two Crystal Awards of Distinction in The Communicator Award 2000 Print Media competition. The Communicator Award is a national awards organization that recognizes outstanding work in the communications field. The Award of Distinction is awarded for projects that exceed industry standards in communicating a message or idea. For more details, see the EMSL Announcement.

PEGASUS code featured on the front page of HPCWire

01/27/00 - The atmospheric chemistry code PEGASUS, featured in the January 21, 2000 issue of HPCWire [http://www.tgc.com/hpcwire.html], was developed by researchers at PNNL to model the fate of energy-related pollutants (such as ozone, nitrogen oxides, sulfur) in the lower part of the atmosphere. This research project was carried out using the MSCF's 512-processor IBM SP.

SuperComputing '99

Abstract, 3D modeled pictures, and a virtual tour of the PNNL exhibit at the 1999 SuperComputing Conference in Portland, Oregon, November 13-19 - Link to photographs of the conference

Molecular Science Software Suite selected by R&D Magazine for R&D 100 Award

06/99 - EMSL's Molecular Science Software Suite-MS³-has been recognized by R&D Magazine as one of the 100 most technologically significant new products and processes of 1999. MS³ is a comprehensive, integrated set of tools that enables scientists to understand complex chemical systems at the molecular level by coupling the power of advanced computational chemistry techniques with existing and rapidly evolving high-performance, massively parallel computing systems. MS³ consists of three components: 1) the Extensible Computational Chemistry Environment (Ecce), 2) the Northwest Computational Chemistry Software (NWChem), and 3) Parallel Software Development Tools (ParSoft).

Second Round of EMSL/MSCF Grand Challenge Projects Selected

04/18/99 - Four proposals selected as Computational Grand Challenge Applications (CGCA) projects in environmental molecular science basic research

Scientific Data Management (SDM) deployment expanded

04/09/99 - After a successful prototyping cycle, EMSL's Scientific Data Management (SDM) software has been deployed to additional EMSL users. The new Windows user interface, developed jointly by EMSL Instrument Development Laboratory (IDL) and SDM staff, makes EMSL's powerful data archival capabilities available to a much broader set of users. Along with EMSL's Computer and Network Services, we have been working closely with staff in Macromolecular Structure and Dynamics (MS&D) to implement a complete solution to their data handling needs. This collaboration addresses multiple computer platforms as well as tools to expand the researchers' access the EMSL data archive, network storage, and analysis applications. SDM and the EMSL scientific data archive-->

High Performance Computing Tools and Libraries Improve HPC Performance

01/15/99 - The high performance computing tools and libraries effort of the EMSL Computing & Information Sciences (C&IS) directorate provides and maintains the parallel computing tools that are integral to building efficient, scalable simulation applications for the MSCF and supercomputers elsewhere. In an ongoing partnership with IBM, EMSL staff is optimizing performance of one-sided communication for noncontiguous data transfers on the IBM SP supercomputers, like our EMSL production system, NWMPP1. For example, we collaborate on and exchange specifications for IBM's Low-level Application Programming Interface library (LAPI). Recently, the Northeastern Center for Parallel Architectures at Syracuse University became an early external user of ARMCI (Aggregate Remote Memory Copy Interface), our new portable one-sided communication library developed under DOE-2000 ACTS project (Advanced Computational Testing and Simulation). Syracuse U. has already incorporated this library into the PCRC (Parallel Runtime Consortium) runtime library supporting research on parallel compilers and languages. They observed a 20-percent improvement in performance of collective operations implemented with ARMCI over the traditional MPI (Message Passing Initiative) approach.

EMSL Scientific Paper Recognized at SuperComputing '98

11/13/98 - A technical paper describing work by three PNNL scientists was named the Best Overall Paper at the 10th annual high performance computing conference, SuperComputing '98, in Orlando Florida. Drs.Holger Dachsel, Jarek Nieplocha, and Robert Harrison submitted and presented the paper "An Out-of-Core Implementation of the Massively Parallel Multireference Configuration Interaction Program" in the Applications session of the conference. The best overall paper at the conference was chosen based on both the written manuscript and the oral presentation. In this paper, the three PNNL authors describe a novel parallelization approach they developed to solve the largest multireference configuration interaction (MRCI) problem ever attempted. MRCI calculations produce highly accurate electronic structure wavefunctions by including extensive electron correlation in the solution of the Schroedinger equation. Using an out-of-core approach, shared memory programming model, improved data compression algorithms, and dynamic load balancing with a time-sorted task list, they were able to solve a problem six times larger than previously reported. Dr. Dachsel worked as a postdoctoral fellow with Dr. Harrison in EMSL's Theory, Modeling and Simulation Directorate. Dr. Nieplocha is in EMSL's Computing and Information Sciences Directorate.

MSCF Announces Call for Proposals for 1999

9/11/98 - The Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory announces a request for proposals (for allocations of computer time) for Computational Grand Challenge Applications (CGCA) projects in environmental molecular science research areas that address the environmental problems and research needs facing the U.S. Department of Energy (DOE) and the nation. CGCA projects can be proposed for periods of one to three years, with the duration being appropriate for the scope of research to be performed. The MSCF has a 512-processor IBM RS/6000 SP system as well as a suite of computational chemisty software (NWChem and Ecce) designed to take advantage of the IBM SP and other computer systems in the MSCF. - Proposals due December 18, 1998, 5:00 pm PST.

First Round of EMSL/MSCF Grand Challenge Projects Selected

04/27/98 - ix proposals selected as Computational Grand Challenge Applications (CGCA) projects in environmental molecular science basic research

NWChem Helping to Advance Biomolecular Research

04/98 - The current issue of enVision magazine (Vol. 13, No. 1, Jan-Mar 1998; URL - http://www.npaci.edu/enVision/) from the NPACI NSF sponsored supercomputer center (at UCSD) has a feature article on "Molecular Science - Greater Computing Power and Collaboration Help Advance Molecular Dynamics Simulations." The article reports research that utilizes nwARGOS from the NWChem suite of programs developed in the EMSL Theory, Modeling, and Simulation organization. The article reports on biomolecular simulations on human acetylcholinesterase (AChE), mouse AChE, HIV integrase, and green fluorescent protein (GFP). nwARGOS is being used in simulations on the latter three research projects, and will be used in the near future for the simulations in the human AChE research. "The new simulations make use of a scalable parallel molecular dynamics code, nwARGOS, part of the NWChem suite of programs from the Pacific Northwest National Laboratory (PNNL) in Washington. The nwARGOS software was developed by former McCammon group member and collaborator Tjerk Straatsma now at PNNL, which is also an NPACI partner."

IBM Solutions Brief Features PNNL - EMSL - MSCF

04/98 - A PNNL/EMSL application brief was published by IBM, and also posted on IBM's web pages . The brief focuses on the advanced simulation studies in molecular science and reactive transport being done at the EMSL to further the scientific understanding of the DOE's and the Nation's environmental problems. EMSL's unique scientific software - NWChem and Ecce for molecular science and MCTRACKER for subsurface reactive transport - are featured also.

Experimental Computing System Installation in MSCF

03/98 - The Northwest Experimental Computing System 1 (NWECS1) is being installed in the EMSL/MSCF during March 1998. The NWECS1 is an IBM SP system with 16 nodes. Each node has four processors. The NWECS1 system will be used to support the strategic scientific software of the MSCF and EMSL.

EMSL Scientists Frequently Cited

01/98 - An analysis of chemistry papers and their citation counts from the Institute for Scientific Information database for the period from 1981 through June 1997 revealed that five EMSL scientists are ranked in the top 1000 of most frequently cited authors.

Name & Organization	Citations	Ranking
Dick Smith, MS&D	5699	121
Dave Dixon, TM&S	3580	378
Bruce Garrett, TM&S	3359	422
Michel Dupuis, TM&S	2765	664
David Feller, TM&S	2621	739

MS&D = Macromolecular Structure and Dynamics
TM&S = Theory, Modeling, and Simulation

Thom Dunning, former EMSL director and Battelle Fellow, was cited 3094 times and achieved a ranking of 517.

Associated Western Universities Board Meeting at the EMSL

01/98 - Associated Western Universities (AWU), Inc., will host its National Board of Directors Meeting at the EMSL in April 1998. The Northwest Division of AWU is coordinating the meeting with staff at the EMSL. Participants will include the AWU National Board of Directors, AWU officers and trustees, the Education and Research Council, and the Education and Research Committee, which consists of approximately 70 senior university officials. EMSL staff will provide overviews and tours of the Wiley Lab to the visitors, many of whom are responsible for research development at their institutions.

EMSL Computer Scientists Demonstrate Capabilities at SuperComputing '97

11/97 - Staff from EMSL research groups and PNNL support organizations produced and staffed a research exhibit at the SuperComputing '97 Conference in San Jose, California (Nov 17-21, 1997). See - SC'97 Abstract & Photos
The research exhibit demonstrated the scientific and technical computing capabilities of the EMSL and several other research groups within PNNL. SuperComputing '97 is sponsored by IEEE and is the premier international conference that focuses on high performance computing and networking. It involves leading researchers, funding agencies, and vendors in the field of computational science. The attendance at this year's conference was 5500. An estimated 1000 attendees visited the EMSL exhibit, thus providing significant exposure of the EMSL's research capabilities to the high performance computing research community.
The display included a network connection to NWMPP1, the IBM supercomputer in the EMSL Molecular Science Computing Facility. Graphics displays and live demonstrations featured the overall EMSL research capabilities, the Collaborative Research Environment (CORE) 2000, the computational chemistry software, DOE's ARM Program, and several examples of computation in the molecular environmental sciences. Interviews of EMSL staff describing the EMSL capabilities will appear in the December issues of ComputerWorld, HPCWire, and Scientific Computing & Automation.

MSCF Request for Proposals Announced

10/97 - The MSCF Request for Proposals of Computational Grand Challenge Applications Projects in Environmental Molecular Science Basic Research - Proposals due January 5, 1998.

Workshop on Subsurface Reactive Transport Modeling

10/97 - A Workshop on Subsurface Reactive Transport Modeling will be held Oct 29 - Nov 1, 1997, in the EMSL Auditorium. The focus of the workshop is on numerical formulations, computational techniques, and solution methodologies for subsurface reactive transport modeling. The workshop is an opportunity for participants to

describe their reactive transport modeling approaches in the context of theoretical, numerical, and computational issues
discuss the accuracy, robustness, and efficiency of their approaches
demonstrate their codes on benchmark problems
use EMSL computers for hands-on instruction.

EMSL-Developed Software Runs on Cray Supercomputer

10/97 - NWChem, a suite of computational chemistry codes developed by staff in the EMSL Theory, Modeling, and Simulation and Computing and Information Sciences research groups, was one of seven applications that was able to efficiently scale and use the computational power of a 1328 processor Cray T3E-900 supercomputer. NWChem was developed to run on the EMSL 512 processor IBM® RS/6000 SP™ supercomputer, so its ability to successfully drive the most powerful supercomputers produced by both IBM and Cray is a strong demonstration of its portability and high parallel performance. NWChem was developed as part of the EMSL Project under funding by the DOE Office of Energy Research and Office of Biological and Environmental Research. More information can be viewed at the NWChem homepage.

Molecular Science Computing Facility About MSCF