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Science and Engineering at The University of Edinburgh

School of GeoSciences

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FAQ

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

Purchasing

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 Fleet.

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.

VPN

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.

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.

Perl

There are many Perl packages that do not come with the "standard install" which you may like to use. We're happy to accomodate requests. If you've asked IT Help to install a Perl module it'll be put into /opt/perl. We use /opt/perl incase there's a clash with the files from the RPMs of the standard install and to stop installed packages clashing with our own Perl modules at a later date.

We may have a different version of a perl module in /opt/perl than that in the standard install. This was most probably due to a request for that version. This is the case for e.g. mod_perl and CGI.pm

To use a perl module installed into /opt/perl in your code you have three options:

  1. Export the PERL5LIB env var to your environment set to /opt/perl
  2. Pass the -I option to perl.
  3. Insert use lib qw(/opt/perl); at the top of your perl program.

These are the current extras packages (mostly) installed into /opt/perl:

  • geos-perl-Module-Build
  • geos-perl-freezethaw
  • geos-perl-Module-Signature
  • geos-mod_perl
  • geos-perl-Digest-SHA
  • geos-perl-ExtUtils-ParseXS
  • geos-perl-cgi-session
  • geos-perl-ExtUtils-CBuilder
  • perl-geos-quota
  • geos-perl-cgi
  • geos-perl-cgi-session
  • perl-term-readkey
  • perl-Net_SSH
  • perl-Archive-Tar
  • perl-io-zlib
  • perl-rss-timing
  • perl-quota
  • perl-net-nis
  • perl-Algorithm-Diff
  • perl-archive-zip
  • perl-Text-Diff
  • perl-tk
  • geos-perl-Image-Size
  • geos-perl-HTML-Template
  • perl-oracle_10

Password Pop Up Boxes

When you log onto a managed Linux box your password provides access to your EASE credentails 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 goto 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 "www.geos.ed.ac.uk" 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


© School of GeoSciences --- Last modified: 16 Jan, 2012 --- Page contact: