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Please note that this page is under construction. We are documenting the 240-node cluster maya that will be available in Spring 2014. Currently, the cluster tara is still available. Please see the 2013 Resources Pages under the Resources tab.
Working with documents and images on tara

Introduction

This page discusses how to work with documents and images on the tara cluster. Several software packages are available for viewing and editing these files. As a prerequisite for most of this discussion, we'll assume you have already set up an X display. Unless specified otherwise, all the packages here are open source, and are standard Linux tools.

Text editors

There are many ways to edit text files on tara. A few of them are

Creating LaTeX documents

LaTeX is the standard tool for scientific publications. It should be possible to write documents entirely on tara using LaTeX. For users who prefer other document authoring software like Microsoft Word, you can of course do your writing on a separate machine.

Here's a minimal example of a LaTeX document

To compile it to a PDF, we can use the "pdflatex" command
[araim1@tara-fe1 ~]$ pdflatex paper.tex
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
... lots of output ...
[araim1@tara-fe1 ~]$ ls
paper.aux  paper.log  paper.pdf  paper.tex
[araim1@tara-fe1 ~]$
To view the resulting PDF, we'll introduce a few more tools below

Creating slides for a talk

Beamer is probably the most popular LaTeX package for creating slides. It is already installed on tara, so let's go through a quick/minimal example. Start with the following document. Compile it using pdflatex
[araim1@tara-fe1 ~]$ pdflatex slides.tex
...
Output written on slides.pdf (3 pages, 52682 bytes).
Transcript written on slides.log.
[araim1@tara-fe1 ~]$
Now you should have a PDF file of your talk
[araim1@tara-fe1 ~]$ ls
slides.aux  slides.nav  slides.pdf  slides.tex
slides.log  slides.out  slides.snm  slides.toc
[araim1@tara-fe1 ~]$ 
In the next section, we will describe some tools for viewing PDFs on tara. Your PDF should look like this.

Note: Some additional UMBC Themes designed by Dr. Rouben Rostamian from the UMBC Department of Math and Statistics are installed on tara.

Creating a poster

Also written by Dr. Rostamian is a package called UMBCposter, which makes it easy to prepare a poster in LaTeX. For details on using the package, see Dr. Rostamian's web site.

The package and its dependencies are installed on tara, and we will show how to compile the example poster on the cluster. First, download the tex file from the author's website.

[araim1@tara-fe1 ~]$ wget http://www.math.umbc.edu/~rouben/umbcposter/sample.tex
...
2010-07-27 06:30:29 (200 MB/s) - `sample.tex' saved [2311/2311]

[araim1@tara-fe1 ~]$
Next compile the poster using pdflatex (the first time it's compiled, the pdflatex command must be run twice).
[araim1@tara-fe1 ~]$ pdflatex sample.tex
...
Output written on sample.pdf (1 page, 36351 bytes).
Transcript written on sample.log.

[araim1@tara-fe1 ~]$ pdflatex sample.tex
...
Output written on sample.pdf (1 page, 36351 bytes).
Transcript written on sample.log.
[araim1@tara-fe1 ~]$ 
Now there should be a PDF file with our poster
[araim1@tara-fe1 ~]$ ls
sample.aux  sample.log  sample.pdf  sample.tex
[araim1@tara-fe1 ~]$ 
See the next section for some ways to view your PDF on tara. Your PDF should look like this.

Viewing PDF files

PDF files on tara can be viewed directly (without requiring a file transfer to your local machine) if you have an X display set up. Browsing a PDF in this way is convenient, but generally much slower than it would be on your local machine. So for browsing long documents, it's recommended to transfer the file to your local machine and view it from there.

gv

gv is a tool for viewing PDF and Postscript files. It generally works quickly over a network connection.
[araim1@tara-fe1 ~]$ gv <pdf_file>

Example of opening our PDF with gv

acroread

acroread is Adobe's non-opensource Acrobat Reader. It can produce a very sharp display of your PDF, but is also generally slow to use over a network connection.
[araim1@tara-fe1 ~]$ acroread <pdf_file>

Example of opening our PDF with acroread

xpdf

Another open source PDF viewer available on tara is xpdf. It is generally quicker to use over a network connection than acroread.
[araim1@tara-fe1 ~]$ xpdf <pdf_file>

Example of opening our PDF with xpdf

Manipulating image files

ImageMagick

ImageMagick is a sophisticated software package for working with image files. It provides APIs for several programming languages, and also some simple commands to use directly. To view an image file, simply type
[araim1@tara-fe1 ~]$ display <image_file>
where <image_file> can be in almost any graphical format. For more information about ImageMagick usage check out this page

GIMP

GIMP (GNU Image Manipulation Program) is an open application for manipulating images. The most basic usage is through the GUI, similar in spirit to Microsoft Paint or Adobe Photoshop. To launch GIMP, simply type
[araim1@tara-fe1 ~]$ gimp
or
[araim1@tara-fe1 ~]$ gimp <image_file>
Here's what it looks like when we open an image. Notice that along with the main image window, we get several other toolbars and menus that we can interact with.

Example of opening an image with GIMP

The first time you launch it, a profile will be created on disk for you. The program will walk you through this process. For more information about using GIMP try "man gimp" at the command line or see its webpage