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.