Computational Software

C/C++

All BMI Linux machines have GCC installed by default in /usr/bin, but that version tends to lag. If you need a more recent version of the compiler — especially if you need C++11 features — you can find more recent compilers in /s/pkg/linux64/gcc. If, for example, you want to use version 4.8.4, just add this to the head of your path: /s/pkg/linux64/gcc/4/8.4/bin.

MATLAB

MATLAB is available on the Linux hosts.

Please do not run more than a single batch job with MATLAB, either directly or through condor. It uses up all our licenses.

Python

There are two paths to Python. First, /usr/bin/python, which is the default system version. Ideally, your path will have /s/bin/python first in your path. This will be more current, and additionally has the packages NumPy, SciPy, SymPy, pandas, Theano, Scikit-Learn and Matplotlib installed. The iPython notebook is also available.

Python 3 is available as python3. As of January 2016, our local Python 3 has all the same scientific packages as Python 2.

Development on Python 2 ends January 1, 2020. After testing, mid-April 2020 will see the final Python 2, at version 2.7.18. We will switch the default /s/bin/python to Python 3 around that April 2020 release date.

R

R, along with many add-on libraries, is installed on all Linux and OSX hosts. The default version is kept fairly current, though in general we do not install versions ending in .0 by default. So, expect R 3.1.1, but not 3.1.0, to be available as the default R. We usually keep a few older versions of R around, callable by version, so R30 for R3.0.1, R31 for R3.1.1.

If you need a new add-on library, and cannot install it yourself, send mail to sysreq@biostat.wisc.edu (link sends e-mail).

SAS

SAS 9.4 is available on the Linux hosts.

Stata

The commands stata (command line) are xstata (GUI) are available on the Linux hosts, at version 13. The special edition versions are available as stata-se and xstata-se.

Julia

The new high-performance language Julia (link is external) is available as an experimental tool on all Linux hosts. For now, Julia is provided as a convenience for those curious about it. If you need it for production purposes, you may want to compile a particular version for yourself in your own project space.

LaTeX

We keep a reasonably current release of the TeX Live (link is external) distribution installed. It has an extraordinary number of packages and styles already installed, but let us know if you need others added.

Git

In addition to the local git client commands, we have an authenticated, web-based interface for git repositories. See Git repository for more information.

Installing R Libraries

While the BCG installs a very large number of R packages by default, from both CRAN and Bioconductor, sometimes people will want to install packages for themselves.See Installing R Libraries for more information.