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GridNexus, a Graphical Interface for Grid Computing

GridNexus, a Graphical Interface for Grid Computing. Ned H. Martin, Department of Chemistry and Biochemistry Ronald J. Vetter, Department of Computer Science Jeffrey L. Brown, Department of Mathematics and Statistics

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GridNexus, a Graphical Interface for Grid Computing

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  1. GridNexus, a Graphical Interface for Grid Computing Ned H. Martin, Department of Chemistry and Biochemistry Ronald J. Vetter, Department of Computer Science Jeffrey L. Brown, Department of Mathematics and Statistics Clayton S. Ferner, Department of Computer Science Andrew J. Martin and Phillip J. Martin, Computer Science students Liberto Bartolotti, Chemistry, East Carolina University University of North Carolina Wilmington SE-SW Regional Meeting of the American Chemical Society Memphis, TN Nov.1-4, 2005

  2. GridNexus

  3. Grid Computing • The idea of Grid computing resulted from the confluence of three developments: • The proliferation of largely unused computing resources (especially desktop computers); over 200 million pcs were sold in the past year! • The greatly increased cpu speed of commodity computers. • The widespread availability of fast, universal network connections (the Internet).

  4. Rationale for a Change The recent proliferation* of fast, interconnectedunderutilized cpus ts/104 * over 200,000,000 pcs were sold last year!

  5. Rationale for a Change • In the summer of 2003, state funding for the North Carolina Supercomputing Center ended, and the Supercomputing Center closed. • The lease for the largest computer, a 720 processor IBM parallel computer, was terminated. • Other smaller machines were distributed to the larger campuses of the UNC system.

  6. Rationale for a Change • High performance computers (formerly called supercomputers) are very expensive to buy and maintain. • Much of the enhancement of computing power recently has come through the application of multiple cpus to a problem (e.g., NCSC had a 720 processor IBM parallel computer). • Many computing tasks relegated to these (especially massively parallel) computers could be performed by a “divide and conquer” strategy using many slower processors on a Grid.

  7. A computing Grid is analogous to an electrical power grid. The user simply “taps” into the resource (with permission), but is usually unaware of the origin of the resource. Power Grid Analogy

  8. Definition of Grid Computing • Grid computing is a form of distributed computing that involves coordinating and controlled sharing of diverse computing, applications, data, storage, or network resources across dynamic and geographically dispersed multi-institutional virtual organizations. • A user of Grid computing need not have the data and the software on the same computer, and neither must reside on the user’s home (login) computer.

  9. Grid Computing • The term "grid computing" suggests a computing paradigm similar to an electric power grid - a variety of resources contribute into a shared "pool" for many consumers to access on an as-needed basis. • Ideally the user does not know or care where the computing operation is being performed; the process is invisible to the user. • Grid middleware handles security, authentication, authorization, resource selection and routing of input and output seamlessly.

  10. Limitations of Grid Computing • Currently, although efforts are being made to standardize protocols (e.g., Globus toolkit and Avaki), interacting with Grid services remains a complex process. • Most of the existing applications that access Grid services require the user to type cumbersome commands, often using a command-line interface. • Creating new clients and services requires programming in a language such as C or Java and using a host of libraries for interacting with Open Grid Services Infrastructure, Grid Security Infrastructure, Web Services Description Language and other standards.

  11. Grid Computing at UNCW • These tools and techniques are useful to a select group of computing specialists; however the only way to make Grid resources accessible to a wide range of users is to provide a relatively simple graphical user interface (GUI). • The UNCW Grid project is developing a GUI that is easy to use and can access a wide range of applications. • Our hope is to create an interface to Grid computing that accomplishes what Internet browsers (Netscape and Internet Explorer) did to open up the WWW .

  12. Grid Computing at UNCW • UNCW mathematics and computer science faculty and undergraduate students, partnered with faculty and students in several “application areas” are developing a graphical user interface (GUI) called GridNexus. • GridNexus serves as a front-end to simplify data manipulations, searching or calculations of various types performed on remote computers over a Grid. • GridNexus is based on JXPL, a new graphical programming language developed by UNCW mathematics and computer science faculty and their students.

  13. GridNexus • GridNexus allows users to link pre-built ‘modules’ that perform various operations into a usable ‘workflow’, then save this workflow for later use. • Once a workflow has been created, only the path/filename of the data set and the path/filename for the output file need to be specified. • This greatly simplifies repetitive operations, and takes much of the mystery (and misery) out of remote computing for non-computer science users.

  14. File Interconversion in GridNexus • One of the limitations of most computational chemistry software packages is that they do not read or write many different (proprietary) file types, so it is difficult to transfer data from one program to another. • GridNexus allows users to input the most common types of geometry specification (.pdb and .mol files) and use a default set of options (or select from a list) to write a Gaussian input file (.dat or .com). • Other transformations are also available.

  15. Gaussian 03 under GridNexus This workflow allows input of a .ENT file, reorientation of the structure, and submission for Gaussian 03 calculation

  16. Molecule Orientation in GridNexus • This module allows a molecule to be oriented in Cartesian space in a specified way, then writes a Gaussian03 input file. origin

  17. Gaussian 03 Input File • %chk=tmp/martinn/phenanthreneNH2.chk • # HF/6-31G(d,p) opt freq • phenanthreneNH2 • 0 1 • H -1.963715 -3.198017 1.280991 • C -1.127512 -2.730904 0.750482 • H -0.184242 -4.593909 0.244859 • C -0.149560 -3.501921 0.166986 • C 0.000000 -0.715690 0.000000 • N 0.000000 0.715690 0.000000 • C 0.908090 -2.892498 -0.536779 • C -1.036579 -1.338948 0.691052 • C 0.971979 -1.491079 -0.702775 • C 1.943981 -3.742718 -1.057698 • H -1.800364 -0.744862 1.210005 • H 1.238823 1.070292 -1.769705 • C 2.993024 -3.223318 -1.730309 • (etc.) Note C & N along the Y axis, the midpoint of their bond at the origin

  18. Gaussian 03 under GridNexus Submitting a Gaussian job can be as simple as selecting the input file name (from a variety of file types) and the desired output file name.

  19. Remote Computing before GridNexus • Before GridNexus, steps to submit a calculation to a remote computer: • Telnet to remote computer, login (separate login and password for each user account and for each computer) • FTP input data file from local computer to remote machine (requires another login, password) • Create and edit an input file for job (using vi or other text editor) • Create a .job file, edit it if necessary • Select queue based on # cpus and time required; submit .job file • Check progress of calculation by periodically: telnet to remote machine; look for file that indicates completion of job. • FTP output file to local computer • Open output file in text editor, examine numerical data • Open output file in a commercial program on local computer to visualize structure

  20. Remote Computing under GridNexus • Now, to submit a calculation to a remote computer on the Grid: • Login to GridNexus (single user login and password allows access to ANY permitted Grid resource via proxy) • Select a data file and job parameters from pull-down menus; click to submit .input and .job file is created automatically by Grid middleware, job is submitted automatically to an appropriate available computer. Upon completion of computation, output file is automatically sent to local computer to visualize structure (which can also be automated).

  21. What’s next for GridNexus? • Develop more “filters” to transform data. • Enhance the graphics for appearance and usability. • Include more software applications. • Extend Grid services to other disciplines. • Include industry and businesses as users and developers. • Add more computational nodes to the Grid. • Make GridNexus available as open source software.

  22. Acknowledgements • UNC-Office of the President • UNCW College of Arts and Sciences • UNCW Division of Academic Affairs • UNCW Department of Chemistry and Biochemistry • UNCW Information Technology Systems Division (ITSD) • Microelectronics Center of North Carolina (MCNC)

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