Software to Install on Personal Computers

I’ve been working lately with some visiting students, people outside the research group, and new students within the group that need to install some software on a personal laptop to get started.  Here is a guide to what you need to install. (Last Updated January 20, 2012).

  • (Required, Available to ANGEL Group Members Only)  If you haven’t already done so, contact Josh Kollat to become part of the AeroVis user group on Penn State’s ANGEL course management system,  There, you can download AeroVis, which is the visualization software that we use.  Also grab a copy of the sample data files and documentation which are really helpful.
  • (Required, Available to Everyone) Cygwin is used to connect to the cluster and see visual programs such as Matlab that are running on the cluster.  It can be found at  Download setup.exe and save it in a place (such as your Documents folder) where you will remember where to find it, since you may need to run it again.  Double click on setup.exe to get started.  You can either select the “default” packages when it asks which packages to install, or go ahead and select “all” to install all packages.  Either way, you may have to go back and select additional packages in subsequent runs of setup.exe if everything doesn’t install right.  The main package we’ll be using is “X-Window”, but according to their website, you install X-Window by following the same process of installing the cygwin package.  This is probably the hardest of any of the software packages to install, and it takes a long time.  Let us know if you need any help, and you can leave a comment if you have any tips on how to make the install process easier.  Afterwards, change your windows environment variables to add ;C:\cygwin\bin to your windows path. Note: Ryan has some additional ideas about the best way to access remote computers. Stay tuned for his post on the subject, and he can edit this post too with more details.
  • (Required, Available to Everyone) You’ll need a text editor, such as Notepad++ or PSPad.  Try both and see which one you like better, they are both free.  While you can use notepad or wordpad to do a lot of the text editing, these programs are a lot more comfortable for working with data and programming.
  • (Required, Available to Everyone) Use WinSCP for file transfer to the cluster.Ryan’s suggestions will probably pertain to this advice too. I know Matt and Ryan use different software packages so I’d love their input here. See comments to this post for additional discussion about this.
  • (Required Only for Visiting Students who Need College of Engineering Wireless) A group member can contact Bob White to get access for you.  A Penn State student must download software at the college’s site and load it on the visitor’s laptop.
  • (Required for Most Students Publishing Papers and Writing Theses Internally in the Group) You’ll need a LaTeX system. LyX is an open source “document processor” that has compatability with LaTeX. Please add additional suggestions for LaTeX environments and editors, preferably ones with syntax highlighting and some graphical features (such as adding equations using symbols). We have a license for WinEdt, but it’s not free for personal use.
  • (Optional, Available to Everyone)  Open source tips:  When in a Penn State computer lab or at a computer in our office, you can use Adobe Photoshop and Illustrator for figure editing and Microsoft Office products.  If you want access to some nice programs on your personal computer, though, for free, try Inkscape (for vector images), GIMP (for raster images and pictures), and Open Office (an alternative to Microsoft) which are all freely available.
  • (Optional, Available to Penn State Students Only) Some good software is available at  Secure Shell Client, under “File Transfer” at that site, is a file transfer/terminal program used to connect to the cluster.  Different people have varying preferences for file transfer and cluster stuff.  I personally recommend WinSCP and running terminal commands on Cygwin, so Secure Shell is not really required.

As far as software that costs money or for computers in the office, we would generally need Microsoft Office, Microsoft Visual Studio, Matlab, and the Adobe Suite.  Students shouldn’t have to worry about installing those programs on their personal computers.  If you get Cygwin working correctly, your cluster access will allow you to use Matlab, Mathematica, programming compilers, and other software, so even if you don’t have access to your own copy of Matlab, you can use it interactively on the cluster.

Let me know if you have any questions by emailing jrk301 at


5 thoughts on “Software to Install on Personal Computers

  1. Pingback: The Cluster and Basic UNIX Commands « Pat Reed Group Research Tips Blog

  2. This comment applies to Windows programs, specifically.

    This is a matter of taste, but I don’t have a whole lot of use for GUI file transfer programs, and I usually end up using Cygwin’s command-line sftp. (Which works just like the Mac version I described in my post.)

    As far as LaTex environments go, TexLive gives you the kitchen sink as far as the backend goes: pdftex, latex, context, luatex, xetex, metafont, metapost, as well as more than 900 packages. TexLive doesn’t come with a GUI, to my knowledge. I like to use gvim and xpdf side-by-side inside cygwin because xpdf doesn’t lock the file, so you can rebuild your pdf and use xpdf as a previewer.

    There’s also MikTex, which can be installed as a portable executable. It takes the opposite approach from TexLive and only downloads a package if you try to use it. MikTex comes with TexWorks, which gives you a basic editor with syntax highlighting, along with a previewer. The two are linked, so you can jump to source from the previewer and vice versa.

  3. Pingback: Compiling MODFLOW2005 on the Janus computing cluster | Water Programming: A Collaborative Research Blog

  4. Pingback: Water Programming Blog Guide (Part I) – Water Programming: A Collaborative Research Blog

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s