How to install Topspin 3.7 on Alma Linux 9 and configure with AVIII/HD consoles
Based on the Bruker guide of how to install Topspin 3.7 on Alma Linux 9, we added the modifications we had to make in order to get the our computer communicating with an AVIII console. This is by no means an extensive guide of all the issues and errors.
- Before You Begin
- Back up your system configuration with nmrsave on Topspin and copy the nmrsave file an external data carrier or network that you can access on the new computer.
- If you are transferring a License from another computer with Codemeter, you MUST follow these steps first to make the license available:
- On the spectrometer computer go to: http://licensecentral-bbio.bruker.de/index.php
- Enter the Ticket Number
- Press Re-Host Licenses
- Press Deactivate License
- Installing the Alma Linux 9
- Download Alma Linux 9.2 (x86_64). It's very important that you install this exact version at first; You can update the kernel after the Topspin installation and proper configurations are done.
- Install Linux as installation type 'Workstation'. The important point here is: if you use DNS naming, you MUST have the computer's name as the same name of the DNS, e.g if you set the hostname on the installation as ' AVIII750', the DNS name has to be aviii750.domainname
- During installation of the OS, create a 'nmrsu' user with sudo permissions in order to be able to configure the system later on.
- Reboot after the installation, then login as nmrsu (or your superuser name) and, when asked for password, look for a small cogwheel icon on the bottom right corner of the screen and select 'Standard x11 display server' on Xorg. (We personally prefer the 'Classic with x11' xorg option).
- Preparing to Install Topspin
- The first thing to do is to nano (or vi) /etc/hosts and add the following lines to the file
- 127.0.0.1.name.domain_name
- xxx.xxx.xxx.xxx(computer's IP) name.domain_name
- name is the name of the workstation and domain is the domain of the network
- The following instructions are used to prepare your computer for installation and operation Topspin:
- Open a Linux Terminal and log in as root ("sudo su")
- dnf --nogpgcheck install https://repo-bbio.bruker.com/AlmaLinux/9/Bruker-Addon/bruker-addon-latest.x86_64.rpm (or dnf --nogpgcheck install https://repo-bbio.bruker.com/AlmaLinux/9/Bruker- Addon/bruker-addon-latest.x86_64.rpm)
- dnf config-manager --set-enabled crb
- dnf install epel-release
- dnf install --nogpgcheck https://mirrors.rpmfusion.org/free/el/rpmfusion-free-release-$(rpm -E %rhel).noarch.rpm ( or dnf install --nogpgcheck https://mirrors.rpmfusion.org/free/el/rpmfusion-free-
release-$(rpm -E %rhel).noarch.rpm) - dnf install https://mirrors.rpmfusion.org/nonfree/el/rpmfusion-nonfree-release-$(rpm -E %rhel).noarch.rpm
- Now Install the Environment to install Topspin:
- dnf install --enablerepo=bruker bruker-topspin-environ
- dnf install --enablerepo=bruker bruker-acquisition-environ
- The first thing to do is to nano (or vi) /etc/hosts and add the following lines to the file
- Install and Configure Topspin
- Go to: https://www.bruker.com/protected/en/services/software-downloads/nmr/linux/linux-topspin.html and download the latest Topspin 3.x (It has to be 3.7 or later if available).
- Proceed with the installation; Be sure to install diskless as well.
- Before opening Topspin, check if 'tftp' is enabled as standard, Topspin will use this process to connect to the IPSO.
- To check, open a terminal and run: systemctl status tftp.socket
- If it shows 'inactive' run: sudo systemctl enable --now tftp.socket
- You'll have to do the same for 'tftp.service', on a terminal run sudo systemctl enable --now tftp.service
- Open Topspin and run nmrsave (if you don't have a backup file ignore this step)
- restore the backup using the nmrsave file you created before.
- Do a cf, select the spectrometer configuration added by the nmrsave file, and proceed with the cf configurations. Run edprobe, expinstall and paracon.
- If Topspin was installed as data station mode, follow these steps before executing cf:
- Go to: /opt/topspin3.7.0/conf/instr/Bruker_default_avIII600 and nano (or vi) uxnmr.par find the line with "##$DATSTAT= yes" change to no
- Save and close.
- If Topspin was installed as data station mode, follow these steps before executing cf:
- At this point you should be able to operate the console and acquire data, unless you have a cryoprobe.
- If you have a cryoprobe, close Topspin, open a terminal and login as root ("sudo su")
- To install the requirements to access the cryopanel run:
- /usr/diskless/crco_data/crco-install
- It should show something like "service crco installed" or "service crco enabled" and "NOTE: /usr/diskless/crco_data/crco-install terminated with success"
- Restart the computer again and after it reboots, open Topspin, execute ha, start a soft shutdown and when that is done restart the console.
- Execute cf again - if you did not use nmrsave at the beginning, you'll need to configure the correct TTYL port.
- Now you should be able to access the cryoplataform.