# Software

### A Note about Running Applications

Software on the severs - and indeed on the linux workstations - can be run remotely from any computer. On the linux workstations, this is trivial: simply open a terminal and enter ssh hostname and then run your application.

## Applications on the Departmental Servers

The following mathematical, statistical and general scientific computing applications are available to researchers and graduate students in the department:

If you see anything missing on this page, or would like to suggest links to tutorials, guides, etc. for other users, please notify the RHPCS analysts.

### Maple

#### Description

Maple is a computer algebra system with capabilities that make it a general mathematical computing package as well.

You can run Maple from an terminal or console window. Use maple for the console (text-only) version and xmaple for the graphical version. Older versions can by run by adding the version number to the command; e.g. xmaple11. For instructions for running applications remotely (from home or a laptop), see the Software section of the Computing Resources FAQ.

### MATLAB

#### Description

"MATLAB is a numerical computing environment and programming language. Created by The MathWorks, MATLAB allows easy matrix manipulation, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs in other languages. Although it specializes in numerical computing, an optional toolbox interfaces with the Maple symbolic engine, allowing it to be part of a full computer algebra system." MATLAB in Wikipedia (2007, January 4).

You can run MATLAB from an terminal or console window. Use matlab-console for the console (text-only) version and matlab for the graphical version. Older versions can by run by adding the version number to the command; e.g. matlab2009a. For instructions for running applications remotely (from home or a laptop), see the Software section of the Computing Resources FAQ.

### Octave

#### Description

"Octave is a free computer program for performing numerical computations which is mostly compatible with MATLAB. It is part of the GNU project. Note that Octave is not a computer algebra system. Octave is rather a tool for scientific computation." GNU Octave in Wikipedia (2007, January 10).

### FFTW

#### Description

"FFTW [Fastest Fourier Transform in the West] is a comprehensive collection of fast C routines for computing the discrete Fourier transform (DFT) in one or more dimensions, of both real and complex data, and of arbitrary input size."

### SAS

#### Description

Graphical statistical analysis analysis package

#### Notes

SAS 9.4 is installed on bayes..

### S-Plus

7.0

#### Description

Statistical analysis and visualization package

#### Notes

Only eight S-Plus sessions can be run at one; please don't leave S-Plus running unless you are actually using it. Run using commands 'splus6' or 'splus7'; 'splus' is an alias for 'splus6'.

### R

#### Description

A "Gnu S"

You can run R from an terminal or console window. Use the command R for the latest version or add the version number to the command for an older version; e.g. R-3.1.3. For instructions for running applications remotely (from home or a laptop), see the Software section of the Computing Resources FAQ.

### sm

#### Description

An interactive plotting programme with a flexible command language.

#### Official Site

SM (includes a complete reference manual and handy tutorial)

### PDL

#### Description

"PDL (Perl Data Language) gives standard Perl the ability to compactly store and speedily manipulate the large N-dimensional data arrays which are the bread and butter of scientific computing. ... PDL turns perl in to a free, array-oriented, numerical language similar to such commerical packages as IDL and MatLab. ... A simple interactive shell (perldl) is provided for use from the command line and a module (PDL) for use in perl scripts." Note that PDL is free and can be installed on any workstation with a current version of perl.

### LaTeX

#### Description

LaTeX is a high-quality typesetting system, with features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents.

#### Instructions

LaTeX documents can be prepared in any editor. The easiest way to create a PDF or postscript file from your .tex file is to use the commands pdflatex and pslatex, respectively.

Most of the linux workstations have the lyx, a specialized latex editor, and kile, an more elaborate integrated latex environment, installed.

NB: Beamer is not working on ms.mcmaster.ca just now; use latex on your workstation or a computer server (e.g. anatolius, bayes). KM 2007/01/15

### pine

#### Description

A full-featured non-graphical mail client. Pine on icarus is the preferred and fully-supported way of accessing email in the department.

4

## Applications for Unix/Linux Workstations

Following is information and help relating to popular applications found on many of the unix and linux workstations used by individual researchers or research groups. If you would like one of these applications installed on your workstation, contact the RHPCS analysts.

This list in not exhaustive; information about other applications will be added according to need. Note that many of the applications available on the compute servers are also available on the workstations.

### Maple

#### Description

Maple is a computer algebra system with capabilities that make it a general mathematical computing package as well.

You can run Maple from an terminal or console window. Use maple for the console (text-only) version and xmaple for the graphical version. Older versions can by run by adding the version number to the command; e.g. xmaple11. For instructions for running applications remotely (from home or a laptop), see the Software section of the Computing Resources FAQ.

### MATLAB

#### Description

"MATLAB is a numerical computing environment and programming language. Created by The MathWorks, MATLAB allows easy matrix manipulation, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs in other languages. Although it specializes in numerical computing, an optional toolbox interfaces with the Maple symbolic engine, allowing it to be part of a full computer algebra system." MATLAB in Wikipedia (2007, January 4).

You can run MATLAB from an terminal or console window. Use matlab-console for the console (text-only) version and matlab for the graphical version. Older versions can by run by adding the version number to the command; e.g. matlab2009a. For instructions for running applications remotely (from home or a laptop), see the Software section of the Computing Resources FAQ.

### R

#### Description

A "Gnu S"

You can run R from an terminal or console window. Use the command R for the latest version or add the version number to the command for an older version; e.g. R-2.9.2. For instructions for running applications remotely (from home or a laptop), see the Software section of the Computing Resources FAQ.

### SSH

#### Description

OpenSSH is the new de facto standard for connecting to unix hosts. The programs ssh, scp and sftp replace telnet/rsh, rcp and ftp, respectively. The ssh/scp/sftp programs encrypt connections so that sensitive information (esp. passwords) is not transferred across the Internet in clear text. All unix (incl. linux and OS X) servers and workstations maintained by RHPCS have the ssh tools installed, allowing both outbound and inbound ssh connections.

To be explicit and clear: ssh is the tool you should use for logging in or ftp'ing to any departmental servers, from both on-campus workstations and from home. Telnet and ftp are turned off on on all unix systems that RHPCS manages (except where there are compelling reasons to continue to provide these insecure protocols).

### LaTeX

#### Description

LaTeX is a high-quality typesetting system, with features designed for the production of technical and scientific documentation. LaTeX is the de facto standard for the communication and publication of scientific documents.

#### Instructions

LaTeX documents can be prepared in any editor. The easiest way to create a PDF or postscript file from your .tex file is to use the commands pdflatex and pslatex, respectively.

Most of the linux workstations have the lyx, a specialized latex editor, and kile, an more elaborate integrated latex environment, installed.

### OpenOffice.org

#### Description

OpenOffice.org is both an Open Source product and a project. The product is a multi-platform office productivity suite. It includes the key desktop applications, such as a word processor, spreadsheet, presentation manager, and drawing program, with a user interface and feature set similar to other office suites. Sophisticated and flexible, OpenOffice.org also works transparently with a variety of file formats, including those of Microsoft Office.

#### Instructions

Icons for the OpenOffice applications (Writer, Draw, Calc, Impress) should be found in the Applications menu under Office. You can also run ooffice or any of the applications from the command line or Alt-F2:
 oocalc, oodraw, oowriter, ooimpress. 

If OpenOffice attempts to go through a set-up process each time you use it, remove your existing settings files:
 \rm -r .openeffice* 

#### Hosts

Found on most linux workstations. OpenOffice is not installed on the common servers because it consumes a fair bit of memory.

#### News

Search the Computing News blog for announcements about OpenOffice.

### Intel Fortran 90

#### Notes

In order to run f90, you will first need to set up your environment:

 source /usr/local/intel/fc/9.0/bin/ifortvars.csh 

To use the Math Kernel Libraries as well, you will need to add further settings to your environment (there are 32-bit and 64-bit versions):

 source /usr/local/intel/mkl/8.0/tools/environment/mklvars32.csh source /usr/local/intel/mkl/8.0/tools/environment/mklvars64.csh 

### Intel Math Kernel Library

#### Notes

To use the Math Kernel Libraries as well, you will need to add settings to your environment (there are 32-bit and 64-bit versions):

 source /usr/local/intel/mkl/8.0/tools/environment/mklvars32.csh source /usr/local/intel/mkl/8.0/tools/environment/mklvars64.csh 

### sm

#### Description

An interactive plotting programme with a flexible command language.

#### Official Site

SM (includes a complete reference manual and handy tutorial)

## Applications for Microsoft Windows Workstations

The following applications are for Microsoft Windows users who wish to access the departmental servers.

### PuTTY

#### Description

PuTTY is a free, open-source ssh/scp/sftp client which some people prefer to the ssh.com client. One advantage is that the ssh, sftp and scp clients are each single .exe files, which can all fit on single diskette, which can be simply downloaded and used without having to install anything. PuTTY is great for travelling.

### MiKTeX

#### Description

MiKTeX is an up-to-date TeX implementation for the Windows operating system; it can be downloaded for free.

The wikipedia entry for LaTeX lists a number of WYSIWYG editors.