Overstretched IT support
The problem: Crash during boot
More than a year ago, a few weeks after receiving my new work computer, it failed to reboot after a system update and got stuck early in the boot process. I soon realised I could still start the computer using "safe mode". Strangely, nothing seems to be wrong because when I manually exit safe mode at the end of the boot process, the computer works fine. Our IT department has tried to fix the problem many times without success. I even had to work without a computer for about 3 weeks while it was "under repair". You probably know how much work you can get done without a computer: close to zero.
My computer runs Cubbli 20.04.06LTS, an unofficial Ubuntu spin maintained by the University of Helsinki for internal use. Although you can do bioinformatics on a Windows or macOS computer, Linux is hands-down the first choice. Many bioinformatics developers don't even bother to release their software for Windows. MacOS works mostly fine (since it is also UNIX-compliant OS), but I would have to pay twice the price for the same calculating power.
The computer is a Lenovo P350 with an NVIDIA T1000 graphics card, which I use to address two screens. I mainly need the graphics card for 3D modelling, phylogenetics analysis and similar tasks. This graphics card may have caused the trouble. I initially did not want to buy this model, but since there was a shortage of graphic cards at the time, IT convinced me to swap out my original choice against the T1000.
The solution: Upgrade!
Today, I finally figured out how to fix my problem. I bought an NVMe-stick, swapped out my main drive and installed Vanilla Ubuntu 22.04. The T1000 was present during the installation, and I had a Lenovo screen attached to the HDMI1 and an HP screen to HDMI2. And voila, there are no problems. I automatically installed 3rd part drivers during the installation process, and the installer used the Nvidia 535 driver.
Since my computer runs Ubuntu's relatively old 20.04 release, I also wanted to test a Vanilla 20.04 install. The installation was done exactly as with 22.04, and everything looked the same until the reboot, where the system stalled again at exactly the same spot:
[ 0.145189] ACPI BIO Error (bug): Could not resolve symbol [\_SB.PCIO.SAT0], AE_NOT_FOUND (20210730/dswload2-162)
[ 0.145199] ACPI Error: AE_NOT-FOUND, During name lookup/catalog (20210730/ps object-220)
/dev/nvme0n1p2: clean, 198342/244162560 files, 18453697/976623104 blocks
[ 5.599585]
[ 5.615264] USB 1-1: 2:1: cannot get freq at ep 0x1
The easy solution to my 2-year-old problem would have been to simply upgrade from 20.04 to 22.04. But here it gets interesting: Upgrading from 20.04 to 22.04 has been disabled by our IT department. And guess why? There is apparently some bug in Cubbli, which IT has not fixed for the last two years. 22.04 was released in April 2022. This means that IT had nearly two years to fix the bug, but they either did not bother to fix it or were unable to. This is a typical case of failure demand: they don't fix a problem, and then many secondary issues arise due to the original problem. Then IT is surprised that they have so much work to do. The amount of work time lost trying to fix my computer is easily over one week (not including the many hours I have now spent identifying the problem).
The University of Helsinki lacks the resources to maintain its own Ubuntu spin
Cubbli is IMHO a bad idea. I never understood why UH would want to modify a mainstream Linux distribution. OSes are so complex these days that even the wealthiest company in the world fixes about 100 bugs every month and still doesn't manage to keep hackers out of their own CEOs' computers (https://www.bleepingcomputer.com/news/security/microsoft-reveals-how-hac...). Fiddling with something that you don't fully understand is a risky business. UH should have learned from the Munich experiment. Munich went as far as creating their own Linux distro, a recipe for disaster. Now they went back to the cosy bosom of Microsoft. They were surprised that they needed to pay developers to maintain the custom software they deployed. Who would have thought that software needs to be maintained?
Instead of a fully centrally-managed workstation, UH could install vanilla Ubuntu on those employees' desktops, which require a bit more than a toy operation system. The integration that vanilla Ubuntu offers out of the box (e.g. Active Directory) would be sufficient for our university's purposes. That would free lots of IT resources. For sure, it would have prevented my problems since I am typically quick to upgrade to the next Ubuntu LTS once it becomes available.