FAQ

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

• Editing PDFs
• FireFox Plugins
• Matlab
• VPN
• Scientific Software
• Password Pop Up Box on Linux
• Secure Connection Failed
• Installing your own personal R packages
• Monitoring License Usage

Purchasing

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.

FireFox Plugins

• Java
  On Linux you can find the location of Sun's JVM using the JAVA_HOME environment variable. With this follow the intructions here: http://plugindoc.mozdev.org/linux.html#Java note that your FireFox/Mozilla plugins directory is most likely ~/.mozilla/plugins

  However on 64bit platforms these instructions won't work. In that case follow these ones: http://plugindoc.mozdev.org/linux-amd64.html#java-sun.

  Currently on our 64 bit machines make a symlink to /usr/java/latest/jre/lib/amd64/libnpjp2.so from your plugins directory.

• Flash
  There is no Flash plugin for x86_64 but for 32 bit machines and those with x86_64 architectures whom wish to play they can find intructions for adding Flash support to FireFox here: http://www.mozilla.org/support/firefox/faq#q2.1 note that your FireFox/Mozilla plugins directory is most likely ~/.mozilla/plugins
• PDF/Acrobat Reader
  There is no 64bit PDF reader or plugin. For the adventurous and 32bit users copy /usr/local/Adobe/Acrobat7.0/Browser/intellinux/nppdf.so into ~/.mozilla/plugins and restart FireFox.

Information on the University's VPN service can be found here: http://www.ed.ac.uk/schools-departments/information-services/services/computing/desktop-personal/vpn

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.

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"

Secure Connection Failed

Secure Connection Failed
 
... uses an invalid security certificate

• 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".

Installing your own personal R packages

• 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.

Monitoring License Usage

• geoslm.geos.ed.ac.uk which servers most of our flexlm licenses, including Matlab and IDL
• geoslm2.geos.ed.ac.uk which serves envi licenses for some users