Most software is installed in /usr/local with the binaries in /usr/local/bin. Since /usr/local/bin is in everyones path by default, you should be able to launch any program by just typing its command name. For example, to run Mathematica:

[fisher@kimclust40]$ /usr/local/bin/mathematica
or
[fisher@kimclust40]$ mathematica

Please add your name to whatever additional libraries or programs think we should include

• CLAPACK -
• BOOST -

• ATLAS "Automatically Tuned Linear Algebra Software"
  • version 3.8.1
  • Location: /usr/local/src/ATLAS
  • http://math-atlas.sourceforge.net/
• LAPACK
  • version 3.2
  • location: /usr/local/src/LAPACK
  • For higher performace, use the hybrid LAPACK/ATLAS library in ATLAS
    • /usr/local/src/lib/Linux/liblapack.a)
    • see: http://math-atlas.sourceforge.net/errata.html#completelp
  • http://www.netlib.org/lapack/
• LEDA "Library of Efficient Data types and Algorithms: LEDA is a versatile and easy to use C++ class library for combinatorial and geometric computing."
  • http://www.algorithmic-solutions.com/as_html/products/products.html
  • Location: /usr/local/lib/LEDA-4.3
  • For documentation see: /usr/local/lib/LEDA-4.3/Install/unix.txt
  • LEDAROOT has been set to /usr/local/lib/LEDA-4.3

• Paup
  • version 4.0b10 (command: paup)
• SAS
  • version 9.2 (command: sas)
• Mathematica (ONLY ON KIMCLUST40)
  • command line version 6.0.1.0 (command: math)
  • X-windows version 6.0.1.0 (command: mathematica)
  • NOTE: mathematica only works on kimclust40. It will not run on other cluster computers. You must log into kimclust40 when you want to run mathematica.
• MatLab
  • version R2008a (command: matlab)
• R
  • version 2.7.2 (command: R)

• C/C++
  • gcc version 4.1.2 (command: gcc)
  • gcc version 3.4.6-4 (command: gcc34)
  • gcc version 4.3.2-7 (command: gcc43)
  • intel version 7.0-86 (command: icc)
• Perl
  • version 5.8.8 (command: perl)
• Python
  • version 2.6.1 (command: python)
  • version 2.4.3 (command: python2.4)
  • version 2.3.3 (command: python2.3)

• MySQL
  • Version 5.0.18-standard (command: mysql)
  • You must first contact StephenFisher to create a new database or user account

• SWISS-PROT Our local database is updated monthly
  • Location: /usr/local32/src/BLAST
  • http://us.expasy.org/

• BLAST Our local databases are updated monthly
  • Location: /usr/local32/src/BLAST
  • http://www.ncbi.nlm.nih.gov/BLAST/

• MacClade
  • Version 4.0.5
  • This is installed on the lab Macintosh laptop