NCSI - Parallel/Cluster Workshop - Community Software

Sources of Software, Documents, and Databases

• IEEE Task Force on Cluster Computing - http://www.ieeetfcc.org

• NetLib - http://www.netlib.org

• GNU (GNU's Not Unix) - Free Software Foundation - http://www.gnu.org
  Science packages - http://www.gnu.org/directory/science
  Math packages - http://www.gnu.org/directory/science/math

• Computational Science Education Reference Desk - http://www.shodor.org/refdesk/Resources/index.php

• Beowulf project (mailing list, software, documentation) - http://www.beowulf.org

• OSDN - Open Source Developers Network
  • SourceForge - http://sourceforge.net
  • FreshMeat - http://freshmeat.net
  • Slashdot - http://slashdot.org

• Open Cluster Group (OSCAR) - http://openclustergroup.org

• Google - http://www.google.com

• Your peers

Evaluating Software

• CiteSeer - http://citeseer.ist.psu.edu

• Google's scholar - http://scholar.google.com

• FAQs

• Mailing list archives

• Your peers

The Process

• Packages
  • Download the package
  • RPM - "$ rpm -Uvh [umm]"
  • Others - yum, apt-get, portage

• Tarballs
  • Download the tarball
  • tar zxvf [umm]"
  • Configure - "$ ./configure" (and --help)
  • make
  • make test
  • su
  • make install

Particular Packages

• GNUmp

• Molecular Dynamics
  • GROMACS - http://www.gromacs.org
  • NAMD - http://www.ks.uiuc.edu/Research/namd

• Linear Algebra
  • LAPACK - http://www.netlib.org/lapack
  • Trilinos - http://software.sandia.gov/trilinos
  • High-Performance BLAS - http://www.cs.utexas.edu/users/flame/goto

• PETSc (PDE and ODE) - http://www-unix.mcs.anl.gov/petsc/petsc-as (parallelized with MPI)

• FFTW (Fastest Fourier Transformation in the West) - http://www.fftw.org (parallelized with MPI)

Educational Resources

• NCSA's on-line tutorials (MPI, cluster computing, etc.) - http://webct.ncsa.uiuc.edu:8900

• Robert Brown's book - http://www.phy.duke.edu/~rgb/Beowulf/beowulf_book.php

Other

• Cite the tools you use in your papers, most have a description (and BibTex source) for how they would like it done.

• Numerical Recipes - Not free but often a reasonable starting point if nothing else is available. http://www.nr.com

• A couple of words about open generally: source, scholarship.
  • Eric Raymond's "The Cathedral and the Bazaar".
  • The President's Information and Technology Committee (PITAC) reports.