Accelerating Scientific Discovery Through Computation and Visualization II
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Volume 107, Number 3, May–June 2002 Journal of Research of the National Institute of Standards and Technology [J. Res. Natl. Inst. Stand. Technol. 107, 223–245 (2002)] Accelerating Scientific Discovery Through Computation and Visualization II Volume 107 Number 3 May–June 2002 James S. Sims, William L. George, Steven Robert B. Bohn This is the second in a series of articles de- G. Satterfield, Howard K. Hung, John G. National Institute of Standards and scribing a wide variety of projects at NIST Hagedorn, Peter M. Ketcham, and Terence Technology, that synergistically combine physical sci- J. Griffin Gaithersburg, MD 20899-001 ence and information science. It describes, National Institute of Standards and through examples, how the Scientific Ap- Technology, Adele P. Peskin plications and Visualization Group (SAVG) Gaithersburg, MD 20899-001 at NIST has utilized high performance par- National Institute of Standards and allel computing, visualization, and machine Technology, Stanley A. Hagstrom learning to accelerate research. The exam- Boulder, CO 80305 ples include scientific collaborations in the Department of Chemistry, following areas: (1) High Precision Ener- Indiana University, and gies for few electron atomic systems, (2) Bloomington, Indiana 47405 Flows of suspensions, (3) X-ray absorption, Yolanda M. Parker and Judith E. Devaney (4) Molecular dynamics of fluids, (5) Julien C. Franiatte and Garnett W. Bryant National Institute of Standards and Nanostructures, (6) Dendritic growth in al- National Institute of Standards and Technology, loys, (7) Screen saver science, (8) genetic Technology, Gaithersburg, MD 20899-001 programming. Gaithersburg, MD 20899-001 [email protected] W. Jasko´lski [email protected] Key words: discovery science; FEFF; Instytut Fizyki UMK, [email protected] FeffMPI; genetic programming; Hylleraas- Grudziadzka 5, [email protected] Configuration Interaction; immersive envi- 87-100 Torun, Poland [email protected] ronments; Lennard-Jones; nanostructures; [email protected] screen saver science; parallel computing; Nicos S. Martys, Charles E. Bouldin, [email protected] QDPD; scientific visualization. Vernon Simmons, Oliver P. Nicolas, James [email protected] A. Warren, and Barbara A. am Ende [email protected] [email protected] Accepted: May 15, 2002 National Institute of Standards and [email protected] Technology, [email protected] Gaithersburg, MD 20899-001 [email protected] Available online: http://www.nist.gov/jres [email protected] John E. Koontz and B. James Filla [email protected] National Institute of Standards and [email protected] Technology, [email protected] Boulder, CO 80305 [email protected] [email protected] Vital G. Pourprix [email protected] National Institute of Standards and [email protected] Technology, [email protected] Gaithersburg, MD 20899-001 [email protected] Stefanie R. Copley National Institute of Standards and Technology, Boulder, CO 80305 223 Volume 107, Number 3, May–June 2002 Journal of Research of the National Institute of Standards and Technology 1. Introduction 2. Immersive Scientific Visualization The process of research may be abstracted into three The Immersive Visualization (IV) laboratory plays a major components as shown in Fig. 1. Increasingly ex- key role in accelerating scientific discovery. The NIST periment means computational experiment as comput- scientist views their serial/parallel computation results ers increase in speed and memory. Parallel computing or experimental data with our IV system. The advanced assists in this by providing access to more processors visualization provided by virtual reality techniques in and more memory. Consequently more complex models our IV environment provides greater insight into large, that run in feasible times become possible. Laboratory complex data sets by allowing the scientist to interac- experiments as well are becoming parallel as combina- tively explore complex data by literally putting the sci- torial experiments become more common. Both of these entist inside the data. lead to large datasets where analysis benefits greatly Fully immersive scientific visualization includes: one from visualization. or more large rear projection screens to encompass pe- ripheral vision, stereoscopic display for increased depth perception, and head tracking for realistic perspective based on the user’s viewing direction. The NIST IV laboratory is configured as an immersive corner with two 2.44 m ϫ 2.44 m (8 ft ϫ 8 ft) screens flush to the floor and oriented 90 degrees to form a corner. The large corner configuration provides a very wide field of Fig. 1. Abstraction of research loop. peripheral vision. It is also important for the sense of immersion for the screens to be flush with the floor. The In this paper we describe research collaborations, be- system fulfills the other immersive characteristics with tween members of the Scientific Applications and Visu- stereoscopic displays and head/wand tracking hardware. alization Group (SAVG) and scientists in other labs at Large and complex data sets are becoming more com- NIST, that incorporate parallel computing and visualiza- monplace at NIST, as high performance parallel com- tion as integral parts of the research process. The paper puting is used to develop high fidelity simulations, and is organized as follows. First, in Sec. 2 we describe our combinatorial experimental techniques are used in the immersive environment. 3D immersion greatly assists in laboratory. IV is significantly different from traditional understanding data by literally putting the viewer inside desktop visualization and significantly more effective at their data. It is used in almost every project we do. In illuminating such data sets [1]. One analogy for describ- Sec. 3 we describe a computational measurement that is ing this difference is to consider the difference between not only the most accurate in the world but also extensi- viewing the fish in a fish bowl and swimming with the ble to larger systems. Following, Sec. 4 describes com- fish at their scale. However, the benefits of IV can only puter simulations of complex fluids like suspensions. be gained when scientists use it. The key ingredient to We present results for concrete. Parallel computations of making IV accessible to scientists is to provide the abil- the near edge structure of clusters of atoms are given in ity to simply and quickly move their data into the im- Sec. 5. Replicated data parallelizations of molecular dy- mersive environment. namics simulations of fluids are presented in Sec. 6. We The primary software controlling the NIST IV envi- describe parallel algorithms for constructing nanostruc- ronment is an open source system named DIVERSE tures as well as visualization of these structures in Sec. (Device Independent Virtual Environments—Reconfig- 7. Section 8 details our simulation of the solidification urable, Scalable, Extensible) [2, 3]. The DIVERSE API process of a binary alloy. Screen saver science, Sec. 9, (Application Programming Interface) facilitates the cre- is our name for our distributed computing project, de- ation of immersive virtual environments and asyn- signed to harvest the cycles of computers across NIST chronous distributed simulations by handling the details when they are in screen saver mode. Lastly, in Sec. 10, necessary to implement the immersive environment. we discuss the NIST genetic programming system. Cur- The software runs on a variety of display devices from rently it is being used to automatically generate func- desktop systems to multi-wall stereographics displays tional forms for measurement errors. with head tracking. Included with DIVERSE is an extensible application called Diversifly that allows various techniques for nav- igation through user data loaded from a variety of exter- nal data formats. On top of this DIVERSE/Diversifly 224 Volume 107, Number 3, May–June 2002 Journal of Research of the National Institute of Standards and Technology infrastructure, SAVGhas developed additional tools and write the .iv file, the approach followed here allows a techniques for quickly moving research data into the IV user to concentrate on their application by simplifying environment, often with little or no special-purpose the graphics data format to essentially what they are graphics programming. The approach used is to apply already doing. Again, the simplicity of this approach the classic UNIX1 philosophy [4] of creating small and provides quick access to the IV environment for a range reusable tools that fit into the immersive environment of applications requiring the display of colored spheres. and which lend themselves to combination in a variety of Now that this tool has been added to the tool box, it can ways to perform useful tasks such as moving the results be combined with the .seq file format to produce other of a numerical simulation into the immersive environ- types of time series animations. ment. In addition to using DSOs for adding new graphics Using this philosophy, SAVG is providing the key file loaders, they can also be used to extend the function- ingredient to making IV accessible to NIST scientists by: ality of Diversifly. Using this capability, interactive fea- tures can be added. For example, Fig. 2 shows a visual- • developing simple and reusable graphics file formats ization of a cloud water dataset (cloudwater.dx) derived implemented as Diversifly