Information about TopSpin compatibility with AlmaLinux 9

General

Bruker has selected AlmaLinux 9 as successor for the current CentOS 7 distribution which reaches its end of support as of June 30, 2024

Minimal supported Bruker application versions are: TopSpin 4.3 for AV NEO systems and TopSpin 3.7 for AV3 systems.

Older versions of TopSpin are not compatible with AlmaLinux 9. Bruker does not offer support for such combinations.

Who should read this

This information is intended for interested customers who prefer to setup a PC with Linux on their own and do not use a PC that has been delivered preconfigured by Bruker.

Certain preconditions and/or setup steps are required prior to running the installation procedure of TopSpin.

Note that this page is work in progress and may be updated at any time. You may want to come back regularly and check whether there is new information available.

Technical details

We use the AlmaLinux-9 (x86_64) release with the Xfce Environment

Important note for upgrading an existing PC

If you wish to install AlmaLinux on an existing PC that controls your spectrometer, please carry out the following steps.

  1. We strictly recommend executing a scratch installation of AlmaLinux. We do not support any upgrade installations ('Elevation of Distribution')

  2. Back up your TopSpin configuration with nmrsave. Copy the saved configuration to an external data carrier or a network share.

  3. If you are using TopSpin 3.5 with FlexLM license, migrate to CodeMeter. TopSpin 3.7 does not support FlexLM licences.

  4. Deactivate your CodeMeter licenses. This is an important step. Failure to do so would result in the loss of your licenses. The entire procedure is described in the CodeMeter manual supplied with TopSpin (Chapter 4 "Moving an installed license to a different computer - Re-Hosting"). This document is also available online.

Installation

Alma Linux 9

  1. Get an installation media with the newest avaiable AlmaLinux 9 release from https://almalinux.org (Alma Linux).

    The AlmaLinux 9.x release is available here: https://mirrors.almalinux.org/isos/x86_64/9.x.html. Please note that an OS update (with dnf upgrade) upgrades the computer to the latest OS version. This step should only be carried out after installing TopSpin and activating the corresponding CodeMeter licenses.

  2. Install Linux as installation type 'Workstation'.

  3. Add root password and create first user with full name "PCI/NMR Super User" and user name "nmrsu". Reboot after installation finished.

  4. After reboot log in as "PCI/NMR Super User". Before entering the password click on the cog wheel icon and select "Standard (X11 display server) on Xorg"

    5. Only after installing TopSpin and activating the corresponding CodeMeter licenses:

  5. Open a Linux Terminal and log in as root with command "su" (click on "Activities" to select and open a terminal)

  6. In the terminal execute 'dnf upgrade'. Then reboot the PC and log in again as user "PCI/NMR Super User".

Bruker-Addon Repository

The following instructions are used to prepare your computer for installation and operation of the above-mentioned TopSpin and ParaVision versions and their successors:

The next step is to enable the EPEL and RPM Fusion repositories:

Now you can install the System and TopSpin environment:

For a spectrometer PC the following package is required:

If you open a new shell window the alias dnfb is available as shortcut for dnf --enablerepo=bruker

Then you may install other required packages with dnf. The bruker-repo is not enabled per default,
you must add --enablerepo=bruker to the command line) in order to install Bruker packages.

View Repository Infos

Usage of native nvidia drivers

Caveat: The described procedure is suitable for HP Z4G4, Z4G5 and Z2G9 workstations from Bruker - older workstations may require a different driver

Certain applications require native nvidia drivers, for installation you need to proceed as follows:

dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel9/x86_64/cuda-rhel9.repo
dnf makecache
dnf module install nvidia-driver:535-dkms

Reboot the system afterwards

Installation Caveats

Black Screen after kernel update of AlmaLinux 9.2

A black screen could occur after a system reboot, if a kernel update was performed during dnf update. This was due to a bug in the bruker-system-environ package (version 2.0-2). This was fixed in version 2.1-0

To fix the problem run the following commands in a terminal with root priviliges (Press CTRL+ALT+F2 to get a virtual terminal, if you have a black screen):

dnf install --enablerepo=bruker bruker-system-environ
dnf erase kmod-nvidia, kmod-nvidia-5.14.0-284.el9_2.x86_64
akmods --force

Reboot the system afterwards. If the version string for kmod-nvidia does not fit, run dnf list --installed to get the installed version.

Legacy NVIDIA driver

If legacy NVIDIA drivers are needed for the workstation, the bruker-system-environ package can't be installed, because it would install the current stable version.

In this case, use the bruker-system-environ-base package for your installation and install the nvidia driver separately. For GeForce 600/700 use:

dnf install akmod-nvidia-470xx xorg-x11-drv-nvidia-470xx xorg-x11-drv-nvidia-470xx-cuda

SpectrOS installation for systems with (N)MR spectrometer

By default, AlmaLinux 9 has disabled the key exchange method "sha1".

The installation of SpectrOS fails if there is already a SpectrOS < 4.3.0 present on the spectrometer.

To enable the SpectrOS installation, later savelogs and nmrsave use this action to establish a system-wide change of this setting: Run in a terminal with root privileges

update-crypto-policies --set DEFAULT:SHA1

Use this action to establish a change for the current installation only: Run in a terminal with root privileges

sh /opt/Bruker/spectros/post/updatespectros.sh