SoftwareLibrary
See below for Macintosh and Windows specific software.
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
Programming Libraries
- 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
Software Packages
- 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 R2010b (command: matlab)
- There is a bug in Open GL library that will cause Matlab to crash VNC.
- Disable Open GL: 'opengl neverselect'
- Disable hardware implementation: 'opengl software'
- http://www.mathworks.com/support/tech-notes/1200/1201.html
- R
- version 2.7.2 (command: R)
Compilers
- 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)
Databases
- 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: /lab/repo/resources/BLAST
- http://us.expasy.org/
- BLAST Our local databases are updated monthly
- Location: /lab/repo/resources/BLAST
- http://www.ncbi.nlm.nih.gov/BLAST/
Macintosh
- MacClade: Version 4.0.5