School of GeoSciences

School of GeoSciences


The answers to many Frequently Asked Questions will gradually appear here.


We can advise on choices of hardware and software, but the orders are handled by the Finance Office.

Editing PDFs

Generally people put documents in PDF format because they don't want you to edit them. If you must do so, however, you can use pdftk (PDF Toolkit) on the School's Linux machines, such as Burn. pdftk can do all sorts of things to PDFs, but for joining/splitting files, it's reasonably straightforward.

To make your life easier, put the PDFs you want to manipulate into a single directory (ideally near the "top" of your home directory and without using spaces in the directory name(s) - it's also helpful if you don't use spaces in the PDF file names), and when you connect to Burn (using the NX client), "cd" into that directory.

To join in1.pdf and in2.pdf into a new PDF, out1.pdf:
pdftk in1.pdf in2.pdf cat output out1.pdf

You can also extract (or join together) particular pages from one or more PDFs. In the example above, the PDfs are added to the new file (out1.pdf) in the order they're listed.

If you name the input files so that they "list" in the right order (Section01.pdf, Section02,pdf, Section03.pdf..... Section27.pdf) you can just use a "wildcard", e.g.
pdftk Section*.pdf cat output My_Paper.pdf
will join together all the files with names beginning "Section" and ending with ".pdf" into a single PDF file called My_Paper.pdf

"pdftk" is the program, followed by the list of input files, the "operation" bit is the "cat" (short for "concatenate"), and the "output" keyword designates the next "token" as the output file name.


Information on the University's VPN service can be found here:

Some people experience issues when using the VPN at the same time as trying to access resources they might have at home (like networked printers). If that's the case then IS recommend "split tunnelling". Details of which can be found here Configuring split-tunnelling on the cisco VPN client.

Scientific Software

You can find information all things scientific I/O libraries and visualisation on the SciIO page, including instructions on how to use netCDF, HDF5 and silo. Other Scientific libraries are documented here.

Password Pop Up Boxes

When you log onto a managed Linux box your password provides access to your EASE credentials which last 10hrs. After that you may see a pop up box appear asking you to enter your password again. Some people find this annoying. To stop this prompting go to your menu and look for:

"System->Preferences->More Preferences->Session"
In the new pop up window click on the "Startup Programs" tab and disable the "krb5-auth-dialog" program (this will stop it restarting next time you log in). Then run this command from your shell "pkill krb5-auth-dialog"

Secure Connection Failed

If you get this mesaage in Firefox:
Secure Connection Failed
... uses an invalid security certificate
Try this:
  • Goto: Edit->Preferences->Advanced->View Certificates->Authorities, or on M$ Windows: Tools->Options->Advanced->View Certificates->Authorities
  • Find "The University of Edinburgh" in the list.
  • Select "The University of Edinburgh CA".
  • Click "Edit".
  • Select "This certificate can identify web sites".
If you're on the School's network and you try accessing the site using "www" rather than "" you'll still get this error.

Installing your own personal R packages

On the managed Desktop Windows XP PC's in GeoSciences, R is installed on the network and the library is a read only library. Version 2.12.1 now contains all the packages that are contained in the CRAN respositories, but if you have need to install a package that is not included at the CRAN repository you can install into your own library space. Version 2.12.1 of R will allow you to create your own library at M:/R/win-library/2.12

  • To Add packages that are not already installed, choose the package to install from the "Packages" pull down menu
  • The first time you do this it will prompt you to create M:/R/win-library/2.12 if it doesn't already exist, say "Yes"
  • It will then take its time to create the folders and install the package. It will put up a message saying it can't install to N:/DeptSoftware/SciEng/GeoSciences/R/R-2.12.1/library, but you can ignore that as it will eventually install to your own library. The first time of any session is slow as it tries to install the library to the network first and only tries your library after the network. After that it is a bit more intelligent.
Alternatively, you can download the zip files from the R repositories independently and unzip them into M:/R/win-library/2.12. That way , all you will need to do is load them into R when you need them

Monitoring License Usage

You can check the status of the license servers and license usage here: