Modeling NMR Chemical Shifts by 4kGN8IE

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									   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
GridNexus
              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).
        Rationale for a Change

The recent proliferation* of fast, interconnected underutilized cpus
14000
12000
10000
 8000                                              MIPS
 6000                                              ts/104
                                                   Series2
 4000
 2000
    0
    1960 1970       1980 1990      2000 2010
     * over 200,000,000 pcs were sold last year!
      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.
      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.
Power Grid Analogy

           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.
 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.
            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.
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.
   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 .
   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.
                 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.
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.
Gaussian 03 under GridNexus




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



            origin




   This module allows a molecule to be oriented in Cartesian space
in a specified way, then writes a Gaussian03 input file.
Gaussian 03 Input File
 %chk=tmp/martinn/phenanthreneNH2.chk
 # HF/6-31G(d,p) opt freq
                                       Note C & N along the Y axis, the
 phenanthreneNH2
                                       midpoint of their bond at the origin
 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.)
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.
 Remote Computing before GridNexus

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

Now, to submit a calculation to a remote computer on the Grid:

    1.   Login to GridNexus (single user login and password allows
         access to ANY permitted Grid resource via proxy)
    2.   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).
  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.
               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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