Nevis Additional Software

These are programs available on the Linux cluster that are not part of a standard Linux installation. To see what versions of a package are available, use the module avail command; to keep track of new versions, refer to the Nevis-linux archives.

ROOT

This is a C++-based object-oriented physics-analysis software system. It has replaced CERNLIB as the primary analysis tool in the physics community. Consult the ROOT Web site to learn more about the package.

To use ROOT, you must type

module load root

once per login session, then type

root

to run the program. The module load root command will define the variable $ROOTSYS, and you'll be able to find the various tests and tutorials described in the ROOT documentation in directories $ROOTSYS/test and $ROOTSYS/tutorials.

If may also be helpful to consult this hands-on ROOT tutorial that was first taught at Nevis in June 2001, and has been regularly revised since then. The ROOT Publications page has links to other ROOT tutorials.

For compiling and linking ROOT programs, use the root-config command; type root-config --help for a list of options. A typical invocation might be:

g++ myrootprogram.cxx `root-config --incdir --libs`

You can also integrate using ROOT with iPython.

Geant4

Geant4 is a physics Monte-Carlo simulation written in C++. As of Jan-2006, it is the current standard in general-purpose high-energy physics detector simulations.

To use Geant4 at Nevis, type module load geant4. To learn what versions are available, type module avail geant4. (This is generally a good idea, since Geant4 is massively updated once a year, and the different versions are not always backwards compatible.)

CLHEP

CLHEP is a C++ class library used in high-energy physics. Both Geant4 and ROOT make use of the classes in this library.

If you wish to use the CLHEP classes outside of Geant4 or ROOT, you can do so with the command module load clhep.

Latex

This is a standard software package for document processing. It is widely used in the scientific community, especially since many technical journals directly accept computer files containing manuscripts composed in latex.

Here are some guides to Latex. However, the normal way to compose a Latex document is to obtain one written by someone else and edit it to suit your needs.

Tex and Latex by themselves are text-based document composition utilities. If you want to try a WYSIWYG ("what you see is what you get") graphical-based interface to Latex, you can try the lyx command. Lyx documentation is available from the help menu within that program.

If you just type latex to create your documents, they'll be created in DVI format (see below). That format is now fairly obsolete. You probably want to use pdflatex instead; it's the same as LaTeX, but its output is in PDF format.

dvips

When you run LaTeX (as opposed to pdflatex; see above), the program creates an output file in DVI (DeVice Independent) format (the command latex myfile.tex will generate the output file myfile.dvi). This file must be translated into Postscript or some other graphics display language. The basic utility to do this is dvips. You can find detailed documentation here, but basically you just type

dvips -o myfile.ps myfile.dvi

to create the Postscript file myfile.ps.

Viewing a PDF file

Once you've create a Postscript or PDF file, you'll want to view it. The simplest way to do this in Linux is with the evince command:

evince myfile.pdf

Java

If you want to run Java on the Linux cluster, I suggest you try gcj, the Java compiler that's part of GCC. In addition, Sun's Java Development Kit is installed on every system on the linux cluster. See the FAQ if you're just trying to get the browser plug-in to work.

OpenOffice

The OpenOffice suite is available on every machine in the Nevis Linux cluster. It includes packages for word processing, spreadsheets, drawing, presentation, and personal information management. It can read and write files created by Microsoft Office.

While it's foolish to claim that OpenOffice has all the features of MS-Office, it has all the functionality that a physics researcher is likely to need -- except for scientific article preparation, for which one would use Latex in any case.

CERNLIB (including PAW, HBOOK, Geant3, Jetset, and Pythia)

This was the world standard for public-domain physics-analysis software during the 1980s and 1990s. To use the current Nevis version of CERNLIB (version 2005 as of May-2006), type:

module load cern

Other versions are also available for legacy users: to see what versions are available, type module avail cern. You can learn more about CERNLIB from their web site.

PAW

To use PAW (the Physics Analysis Workstation) from any X-windows terminal, type paw. To use PAW++, a version of PAW with a graphics interface, type paw++.

Compiling with CERNLIB

To call a CERNLIB routine from a FORTRAN program, you must access the CERN libraries:

gfortran myprog.f `cernlib packlib mathlib kernlib`

PACKLIB, MATHLIB, and KERNLIB contain the basic CERNLIB routines. Other useful libraries are GRAFLIB and GRAFX11 (for making postscript plots), PDFLIB (for parton distribution functions), and GEANT3, HERWIG, LEPTO, and ISAJET (Monte Carlo and event generators). Consult the library documentation for more information.