@node Miscellaneous software, Printing, X windows, Top
@chapter Miscellaneous software

A wealth of software is available on the Unix Cluster.  The following
include @emph{very} brief descriptions of the software together with
pointer to additional documentation.

@menu
* emacs::                       Text editor
* tex::                         
* python::                      
* pact::                        
* ghostview::                   
* matlab::                      
* maple::                       Maple V algebra system
* mathematica::                 Mathematica algebra system
* axiom::                       Axiom algebra system
* Portland Group Fortran::      
@end menu

@node emacs, tex, Miscellaneous software, Miscellaneous software
@section emacs

Emacs is powerful text editor.  If running under X, it will normally
use its own window, so you would start it in the background with

@example
emacs &
@end example

@noindent
To prevent emacs from using its own window, specify the @code{-nw}
option as in

@example
emacs -nw @var{file}
@end example

Emacs is fully documented in @ref{Top,The Emacs
Manual,Overview,emacs,The Emacs Manual}.  However, for most people, 90%
of what they need is covered by the online tutorial which is accessed by
typing @kbd{C-h t} (control-H followed by the letter t) while in emacs.
In addition here's a handy @uref{../../comp/emacs-refcard.ps,reference
card}.  Print this on a duplex printer, if you have access to one.

@c Reference card produced by editing
@c /usr/local/share/emacs/20.3/etc/refcard.tex
@c to include
@c  \special{landscape}
@c  \columnsperpage=3
@c  \vsize 8.2in
@c tex refcard.tex
@c dvips -P www -h tumble.pro -h duplex.pro refcard.tex
@c cp refcard.ps /usr/local/apache/share/htdocs/comp/emacs-refcard.ps

@node tex, python, emacs, Miscellaneous software
@section TeX

TeX is a scientific typesetting package.  We run the teTeX distribution
version 1.0.  This is documented at
@uref{http://w3.pppl.gov/misc/teTeX}.  LaTeX @manref{latex,1} is the
recommended macro package.  The run it, use the command

@example
latex file.tex
@end example

Useful (indispensible) books are:

@itemize @bullet
@item LaTeX, a Document Preparation System, by Leslie Lamport (2nd Ed,
Addison Wesley, 1994)
@item The LaTeX Companion, by M. Goosens, F. Mittelbach, and A. Samarin
(Addison Wesley, 1994)
@item The LaTeX Graphics Companion, by M. Goosens, S. Rahtz, and F. Mittelbach
(Addison Wesley, 1997)
@end itemize

If you have problems running TeX, please check your environment
variables, in particular @code{TEXINPUTS}.  Make sure these do NOT
contain references to @file{/usr/local/share/texmf/...},
@file{/usr/local/lib/texmf}, etc.  If you have private macro files in
@file{~/tex}, then you will want to define

@example
TEXINPUTS=.:~/tex: export TEXINPUTS
setenv TEXINPUTS .:~/tex:
@end example

@noindent
in sh or csh syntax.  (The default @code{TEXINPUTS} will be implicitly
inserted after the trailing colon).

This version provides better support for producing documents for online
viewing:

@enumerate
@item pdflatex produces a pdf file instead of a dvi file.
@item the hyperref package has support for carrying the cross-reference
information and references to URLs in a TeX document over to the dvi or pdf
file;  for example, you reference your home page like this

@example
\href@{http://w3.pppl.gov/~jsmith@}@{J. Smith@}
@end example

@item xdvi can follow links (cross-refs and URLs).
@end enumerate

The following are possible ways of producing pdf files from LaTeX

@enumerate
@item In the @file{.tex} file, put

@example
\usepackage@{times@}
\usepackage@{hyperref@}
@end example

@noindent
Process with @code{latex}, then with @code{dvips -Pwww -z}, then with
@code{distill}.

@item In the @file{.tex} file, put

@example
\usepackage@{times@}
\usepackage[dvips]@{hyperref@}
@end example

@noindent
Process with @code{latex}, then with @code{dvips -Pwww}, then with
@code{distill}.

@item In the @file{.tex} file, put

@example
\usepackage@{times@}
\usepackage[pdftex]@{hyperref@}
@end example

@noindent
Process with @code{pdflatex}.
@end enumerate

When you view the @file{.dvi} file produced in method (1) with
@code{xdvi}, the links will be underlined (and you click on them to
follow them).

@node python, pact, tex, Miscellaneous software
@section python

Python is an interpreted, interactive, object-oriented programming
language.  Version 1.5.1 is installed on the Unix Cluster (under
@file{/usr/local}) and on hecate (under @file{/usr/pppl}).

The main documentation is @manref{python,1}.  The web site is
@uref{http://www.python.org}.  There's a reference manual available at
@linuxdoc{python-1.5.1/Doc/ref/ref.ps}.  Our local expert is
@email{hammett@@pppl.gov,Greg Hammett}.

In addition we have the LLNL Python Extensions (release 6) installed.
These are describe at @uref{http://xfiles.llnl.gov/python.htm}.
In order to use these you will need to specify

@example
PYTHONPATH=/usr/local/lib/python1.5/NumPy export PYTHONPATH
@end example

@noindent
The extensions that we have installed are

@itemize @bullet
@item Numerical: provides a fast numerical facility for Python
@item Graphics: enables use of @manref{gist,1} from Python 
@item PyPDB: an interface to PACT/PDB database files. @xref{pact}.
@item PyHistory:  time history data from Python simulations
@item RNG: random number distributions for Python
@end itemize

@node pact, ghostview, python, Miscellaneous software
@section pact

pact is a ``portable  application code toolkit''.  See
@uref{http://www.llnl.gov/def_sci/pact} for details.
To use this at PPPL, you will need
@example
PACT=/usr/local/pact export PACT
@end example

@node ghostview, matlab, pact, Miscellaneous software
@section ghostview

ghostview is a viewer for PostScript and PDF files.  It may be invoked
as gv or ghostview.  We are running version 3.5.8.  Documentation is via
the man page @manref{gv,1}.  There is also documentation available at
@linuxdoc{gv-3.5.8/gv.html}.  The main web site is
@uref{http://wwwthep.physik.uni-mainz.de/~plass/gv/}.

@node matlab, maple, ghostview, Miscellaneous software
@section MATLAB

(From the documentation:)

MATLAB is a high-performance language for technical computing. It
integrates computation, visualization, and programming in an easy-to-use
environment where problems and solutions are expressed in familiar
mathematical notation. Typical uses include:

@itemize @bullet
@item Math and computation 
@item Algorithm development 
@item Modeling, simulation, and prototyping 
@item Data analysis, exploration, and visualization 
@item Scientific and engineering graphics 
@item Application development, including Graphical User Interface building 
@end itemize

To run MATLAB, type

@example
matlab
@end example

We are running version 5.3 (also known as Release 11).  Matlab is
supported on all the computers in the Unix Cluster.  PPPL has a single
floating license for this product.  However, if this license is in use,
MATLAB will automatically use one of the Princeton University licenses,
which should only be used for educational purposes.

Documentation is obtained from @manref{matlab,1}, the command
@code{matlabdoc} (type @code{matlabdoc -h} for documentation), and at
@uref{http://w3.pppl.gov/misc/matlab/helpdesk.html}.  The last includes
manuals in PDF format.  You can see many examples of using MATLAB by 
typing @code{demo} when running the program.

The vendor's web site is
@uref{http://www.mathworks.com/products/matlab/}.

@node maple, mathematica, matlab, Miscellaneous software
@section Maple

Maple is a system for doing algebra.  We are running Maple V Release 5
under a University Site which lets it be run on any Unix Cluster machine
(as well as PC's, personal Linux machines, etc.)  The are two interfaces

@itemize bullet
@item text-only---accessed with the command @code{maple} (see @manref{maple,1})
@item graphical---accessed with the command @code{xmaple} or @code{maple
-x}
@end itemize

The main documentation for Maple V are the books published by
Springer-Verlag (1991--91):

@itemize bullet
@item Maple V, First Leaves: A Tutorial Introduction
@item Maple V, Language Reference Manual
@item Maple V, Library Reference Manual
@end itemize

In addition to the man pages, the graphical interface has a @code{Help}
menu.

The vendor's web site is @uref{http://www.maplesoft.com}.

@node mathematica, axiom, maple, Miscellaneous software
@section Mathematica

Mathematica is a system for doing algebra.  We are running version
3.0.2.  PPPL has a 4-user node-locked license for taurus.  It can also
be used for educational purpose on other Solaris systems using one of
the Princeton University licenses.  There are two interfaces

@itemize bullet
@item text-only---accessed with the command @code{math} (see @manref{math,1})
@item graphical---accessed with the command @code{mathematica} (see
@manref{mathematica,1})
@end itemize

The main documentation for Mathematica is the book ``Mathematica, a
System for Doing Mathematics by Computer'', by Stephen Wolfram,
Addison-Wesley (1988).

In addition to the man pages, the graphical interface has a @code{Help}
menu.

The vendor's web site is
@uref{http://www.wolfram.com/products/mathematica/}.

@node axiom, Portland Group Fortran, mathematica, Miscellaneous software
@section axiom

axiom is a system for doing algebra.  We are running version 2.1.  PPPL
has a site license as part of the NAG Academic Site License Initiative.
It can be run on any Unix Cluster machine and on Linux and Windows PCs.
To run it, type @code{axiom} (see @manref{axiom,1}).  This brings up a
documenation browser.  It's also documented in the book ``Axiom, the
Scientific Computation System'', by Richard Jenks, and Robert Sutor
(Springer-Verlag, 1992).

The vendor's web site is
@uref{http://www.nag.com/sumbolic/AX.html}.

@node Portland Group Fortran,  , axiom, Miscellaneous software
@section Portland Group Fortran

Portland Group Fortran are the recommended Fortran 77 and Fortran 90
compilers for Linux.  We share a 5-user license with the Department of
Geodynamics.  We are running version 3.0

Documentation is via

@itemize @bullet
@item man pages: @linuxmanref{pgf77,1}, @linuxmanref{pgf90,1}.
@linuxmanref{pghpf,1}, @linuxmanref{pgprof,1}, @linuxmanref{pgdbg,1},
and @linuxmanref{Xpgdbg,1}.
@item WEB documentation at @uref{http://w3.pppl.gov/misc/pgi}.
@end itemize

The vendor's web site is @uref{http://www.pgroup.com}.