# 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.

For more details and instructions on running the applications from your own desktop or laptop - either on campus or off campus - see Running Server and Workstation Applications Remotely.

## 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

#### Hosts

anatolius, bayes, workstations

#### 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.

#### Vendor Site

### MATLAB

#### Hosts

#### 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.

#### Vendor Site

### Octave

#### Hosts

#### 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).

#### Vendor Site

### 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."

#### Hosts

#### Official Site

### SAS

#### Description

Graphical statistical analysis analysis package

#### Notes

SAS 9.4 is installed on bayes..

#### Hosts

#### Vendor Site

#### Information & Help

- Introduction to SAS (from Cornell University).
- Introduction to SAS: A Tutorial for SAS Version 8.2 (from theUniversity of Virginia; it's based on SAS for Windows, but the data manipluation is very similar)

### SPSS

#### Description

Graphical statistical analysis analysis package

#### Notes

SPSS Statistics 25 is installed on bayes..

#### Hosts

#### Vendor Site

### 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.

#### Hosts

bayes, anatolius, workstations

#### Information & Help

### sm

#### Description

An interactive plotting programme with a flexible command language.

#### Hosts

#### 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.

#### Hosts

#### Official Site

### 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

#### Official Site

#### Information & Help

- TeX Users Group
- Getting Started with LaTeX (from Trinity College, Dublin)
- Beamer at Wikipedia (see 'External links' for tutorials, the home page and the manual)

### 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.

#### Version

4

#### Hosts

#### Official Site

## 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

#### Hosts

gosset,bayes (and most workstations)

#### 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.

#### Vendor Site

### MATLAB

#### Hosts

gosset,freesurface,bayes, (and most workstations)

#### 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.

#### Vendor Site

### 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.

#### Information & Help

### 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).

#### Official Site

#### Information & Help

### 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.

#### Official Site

#### Information & Help

- TeX Users Group
- Getting Started with LaTeX (from Trinity College, Dublin)
- Beamer at Wikipedia (see 'External links' for tutorials, the home page and the manual)

### OpenOffice.org

#### Description

From www.openoffice.org/about:

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.

#### Vendor Site

### Intel Fortran 90

#### Description

#### Hosts

#### Official Site

Intel Fortran Compiler 9.0 for Linux

#### 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

#### See Also

### Intel Math Kernel Library

#### Description

#### Hosts

#### Official Site

#### 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.

#### Official Site

### 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.

#### Official Site