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NWChem/Gamess Workshop

Monday, January 30, 2006 in DTRC T-4 Conference Room

What is it?

NWChem is a computational chemistry software package developed at the Pacific Northwest National Laboratories (PNNL), designed for high-performance parallel computers as well as clusters of workstations.

GAMESS is the general purpose ab initio molecular electronic structure program for performing SCF-, DFT- and MCSCF-gradient calculations, together with a variety of techniques for post Hartree Fock calculations. A summary of GAMESS capabilities can be found at http://www.msg.ameslab.gov/GAMESS/summary.html.

Who is it for?

The intended audience is researchers in the fields of Drug discovery and Computational Biology/Biophysics, a complex process involving the application of many different areas of knowledge. Effective drug discovery requires that professionals have an understanding of the entire process.

Contents

The lectures will cover topics such as

  • An overview of quantum chemistry and the goals of ab initio calculations.
  • Motivation for applying quantum chemistry to biological systems
  • Molecular Mechanics calculations with NWChem
  • QM/MM calculations with NWChem
  • Quantum chemical calculations using both NWChem and GAMESS
  • A comparison of the capabilities of selected programs. An explanation of sample input and output files.
  • Hands on experience creating input files and running calculations with NWChem and GAMESS.
  • ECCE (Extensible Computational Chemistry Environment) is an integrated environment for composing, running and analyzing quantum chemical calculations. It can be interfaced to NWChem as well as Gaussian.

If you want to participate in the hands-on portion of the workshop you will need an account on the Hartwell Center IBM LINUX cluster. Contact Scott Malone for an account and instructions on logging in. Scott.Malone@stjude.org

If you have questions about NWChem or Gamess, contact Antonio.Ferreira@stjude.org

INTRODUCTORY IBM LINUX CLUSTER TRAINING

There are no classes currently scheduled.

The Hartwell Center maintains a 280 processor IBM Linux Cluster to improve the speed of your software applications. This introductory class will provide hands-on examples and the following information:

  • What is a cluster
    - Hardware
    - Software
  • Brief introduction to using Linux
  • What is LSF and how to use it>
  • What applications are available and how to find them
  • How to speed up your application
  • How to get help and more information

After attending the class the user should have a basic understanding of what the cluster is, what applications are currently installed and how to run applications on the cluster.

If you have question about the Linux cluster or the class please contact Scott Malone ( scott.malone@stjude.org ) at x4947.

WRITING MPI PROGRAMS FOR THE LINUX CLUSTER

There are no classes currently scheduled.

The Hartwell Center's new top-500 ranking supercomputer is available to all St. Jude researchers, but making use of its full power requires some skill in parallel programming.  This class will guide users through parallel programming examples based on the widely used MPI (message passing interface) library.  Each participant will have a chance to modify, compile, and run programs of increasing complexity during the class.  Familiarity with the C programming language is recommended, and general programming skill (in any modern language) is required.  To attend, visit http://www.hartwellcenter.org/bio_rescom/cluster/index.php and click on register for classes.  For further information contact John.Obenauer@stjude.org.