We made a few minor changes to the suite of packages we provide on our Ubuntu desktop & compute hosts during the Christmas break.

Some of these changes were done to support one of our new programming courses – Scientific Image Analysis, which runs for the first time in Semester 2. And we’ve also done a bit of tidying to help us prepare for our new Ubuntu 22.04 (Jammy) platform, which we’ll be revealing later in the year.

Read on to find out more.

Ubuntu Packages added

We’ve added the following Ubuntu packages to the suite of packages that we provide on every Ubuntu desktop & compute host:

• mc (aka Midnight Commander): a text-based file browser.
• inxi: a nice tool for showing information about your current host.

These particular packages come from Ubuntu’s own package repositories, so are pretty easy for us to add.

We can add further Ubuntu packages as necessary – ask us and we’ll explore this with you.

Locally-maintained Packages upgraded to new versions

We’ve upgraded the following packages to newer versions:

• Fiji (“Fiji Is Just ImageJ“): This image analysis tool is being used in our new Scientific Image Analysis course in Semester 2. So we’ve upgraded our package to the latest version – 2023.12.11. We’ve also added a desktop launcher to provide a simpler way to run this tool.
• Cloudy: This Astrophysics code has been upgraded to version C23.01, and should also perform a wee bit better than before.
• Singularity: This container platform has been upgraded to the latest version of Singularity CE – 4.0.3. See an earlier blog post of ours for an introduction to Singularity.

These locally maintained packages don’t exist in the official Ubuntu package repositories, so we manage and build our own Ubuntu packages for installing onto our hosts. This requires a bit more effort from us!

Locally-maintaned Packages updated

We’ve also made a few changes to the following locally-maintained packages.

• Anaconda 2023.07: This mega-package provides Anaconda 2023.07 and a bunch of pre-defined conda environments. We’ve updated this package to add in a new sia conda environment to support the School’s new Scientific Image Analysis course..
• CASTEP: We’ve improved the (rather complex) build process for the 3 different versions of CASTEP we currently provide. They behave the same as before, but the accompanying tools & utilities should be a bit cleaner.
• Enzo: This has been rebuilt with compiler optimisations enabled. We’ve also added in basic manual pages for the 2 main codes provided here – enzo.ini & inits.ini.
• QTIPlot: We’ve simplified the way this gets packaged.
• VMD: Ditto. We’ve also added a desktop launcher to provide another way to start this application.
• xthi: This has been rebuilt, and we’ve created some manual pages for this.

Locally-maintained packages deleted

We’ve deleted the following locally-maintaned packages, as we don’t believe anyone has been using them:

• CASA astronomy pipelines
• DL_POLY (molecular dynamics simulator)
• KMOS & VIMOS ESO pipelines. (We provide all of the software you need to install your own ESO pipelines, which is probably a better solution for everyone!)
• nicaea (cosmology package)
• rw05 (data analysis software)
• Splotch (ray tracer)

We can always look at these again if necessary. But it’s a waste of our time maintaining these if nobody is using them!

Ubuntu packages deleted

We’ve also deleted the following Ubuntu packages, as we don’t think anyone needs them any more:

• icedtea-netx: This provides functionality for running Java WebStart. We previously needed this for an old in-house application, which has since been retired.
• openjdk-8-jre: This provided an older version of Java for an in-house application, which has since been retired. We continue to provide Java 11, though we don’t see much use of Java these days!
• Packages for coding with the Go language: We used to use these for some internal tools. We’re not aware of anyone else coding in Go. So we’ve removed these for now to keep things tidy. Please do contact us if you’re using Go and we’ll find a solution for you.

Help!

If you have any questions about any of this, then please contact us:

• You can email the School Helpdesk: sopa-helpdesk@ed.ac.uk
• Alternatively, you can post in the SoPA Research Computing space in Teams.

Recent Ubuntu package updates / Linux & Scientific Computing - Physics & Astronomy by blogadmin is licensed under a Creative Commons Attribution CC BY 3.0