Ubuntu 20.04 Managed Workstation Software

Ubuntu 20.04 image software

This is the definitive list of packages available on the Departmental Ubuntu 20.04 standard image. We will make sure all of these are installed, although some require loading an environment module before you can use them. One such environment module package is Anaconda, a free, easy-to-install package manager, environment manager and Python distribution with a collection of 1,000+ open source packages with free community support.

Unless they are specially marked, the list of Ubuntu 20.04 software and the environment module packages, are 'supported software' which means that they get a high priority for fixing. Where possible, we test they work before rolling out the image and we may do local configuration to make them easier to use. Everything else you may find on the image is unsupported. We will try to fix problems with it where we can but the amount of time we can spend on it is limited and the priority for fixing may be low. If you want to add a package to the supported list, please ask.

There are some packages we support but intend to drop support for in future, perhaps because there is a better alternative. Those are marked as deprecated.

If you want to install extra packages please see the appropriate section of the FAQ.

Can't find what you need? Different software packages are available for other types of managed machine. A listing of all of our available software packages, including those for the Windows machines, is available at this page.

Ubuntu also maintain some help pages themselves which may be of interest.

Chemistry

• AmberTools 20
• Aten 2.1.9
• Avogadro 1.93.0 (launch with avogadro2)
• CDO 1.9 (Climate Data Operators)
• Gaussian
  • Gaussian 16 (restricted access)
  • Gaussian 09 (restricted access)
  • Gaussian 03
• KNIME
• MOE (restricted access)
• NCO (NetCDF Data Operators)
• Open Babel 3.0
• Schrodinger/Maestro 2018 (restricted access)

Compilers/Languages

• gcc/gfortran/g++ 9.3
• Intel C/C++ (versions 2020-2022, restricted access)
• Intel Fortran (versions 2020-2022, restricted access)
• Intel OneAPI (contains Intel C/C++, Fortran, MPI, MKL and many more from version 2021 up)
• Julia 1.7
• Nag Fortran compiler (5.2-7.0)
• NVIDIA HPC SDK compilers
• Perl 5.30
• Python - see Python section for details
• R 4.1 with the following packages pre-installed:
  • abind
  • akima
  • chron
  • cluster
  • emdbook
  • fields
  • lattice
  • maps
  • maptools
  • MASS
  • Matrix
  • mgcv
  • ncdf4
  • nlme
  • openair
  • plotrix
  • plyr
  • Rcpp
  • reshape
  • reshape2
  • RgoogleMaps
  • rJava
  • spam
  • stringr

Desktops

• GNOME
• KDE (unsupported)

Editors

• emacs (v26)
• nedit
• pico
• vim
• xemacs21
• gedit

Email

• Alpine (replaces Pine)
• Evolution
• Thunderbird

Fonts

• Microsoft core fonts
• terminus-font

GIS

• qgis 3.4 (SPRI only)

Graphics

• dia
• GIMP
• Inkscape
• netpbm (Collection of image manipulation tools)
• tgif
• xfig

LaTeX

• TeX and LaTeX (TeXlive)
• TeXmaker

Libraries

• Boost C++ library
• HDF5
• NetCDF
• szlib 2 (compression library)

Maths

• Mathematica 12.0
• Matlab R2021a
• R (as above)

Maths Libraries

• ATLAS (version 3.10.3)
• GNU Scientific Library (version 2.5)
• Intel MKL (version 2020, restricted access)
• Intel MKL as part of OneAPI (versions 2021 and up)
• FFTW3 (single, double, and quad precision)

MPI Libraries

• OpenMPI 4.1.2 for GNU and Intel compilers
• MPICH 4.0.1 for GNU and Intel compilers
• Intel MPI 2021 for GNU and Intel compilers

Multimedia

• GNOME Music
• Rhythmbox (music player)
• xmms2 (music player)
• gxmms2 (GNOME front-end for xmms2)
• VLC

Network/Communication

• gFTP
• Skype
• OpenSSH (usage notes)
• rclone
• rdesktop
• Remmina remote desktop client (replaces rdesktop and VNC clients)
• sshfs

Office

• LibreOffice 6

Other

• Environment Modules (Tcl implementation, version 4.4.1)
• tellico 2.3.8 (collection management program, usage notes)
• tightvnc
• pidgin (instant messaging client)

Plotting

• gnuplot 5.2.8
• xmgrace 5.1.25

Python

We recommend using Anaconda for Python development as it provides a very wide choice of modules and the ability to easily install whatever additional modules you want via the conda package manager. Please read our usage notes.

• Anaconda Scientific Python Distribution for Python 3
• Ubuntu's native Python packages version 3.8 are also installed with the following modules available:
  • GDAL
  • IPython
  • Matplotlib 3.1.2
  • nose
  • Numpy 1.17.4
  • pandas
  • SciPy 1.3.3
  • shapefile
  • shapely

Shells

• bash
• tcsh (deprecated, use bash)
• ksh (deprecated, use bash)
• IPython (ipython3)

Utilities

• bison (version 3)
• xwrits (Typing interruption software for RSI sufferers)
• maven (Software build tool)
• meld (three-way graphical diff)
• pdfsam (simple PDF editor)
• pdfmod (simple PDF editor)
• qpdf (commandline tools for manipulating PDFs)
• tmux
• valgrind 3.15
• Xconv (file conversion software)

Version Control

• bzr
• git 2.25
  • qgit 2.9
  • gitk
• svn 1.13

Viewers

• evince
• gv

Virtualisation

• Virtualbox

Visualisation

• blender 2.82
• GrADS 2.2.1 (Atmospherics only)
• Jmol 14.6
• Pymol 2.3
• Orange is no longer installed by default but anyone can install it from Anaconda: see Orange software page for details
• UCSF Chimera 1.16
• VMD 1.9.3, 1.9.2
• XCrysDen 1.6
• xmakemol 5.16

Web browsers

• Firefox
• Google Chrome
• lynx
• w3m

Restricted Access

Restricted access means that a licence is needed in order to use the software. Usually if you have a licence we can then make the software available. Some of these licences cost money, others require no money but you must sign an agreement before using the software. More details are available by clicking on the link for the package.