how to install topspin 4.08 in ubuntu 19.10

Question

Is anyone can tell me how to install topspin 4.08 in ubuntu 19.10. I currently have the following errors:

NOTE: using DISPLAY=:0.0
NOTE: using TCL_LIBRARY=/tmp/selfgz27981/linux/tcl-8.6.9/lib/tcl8.6
NOTE: using TK_LIBRARY=/tmp/selfgz27981/linux/tk-8.6.9/lib/tk8.6
NOTE: running /tmp/selfgz27981/linux/tk-8.6.9/bin/wish8.6 -f /tmp/selfgz27981/xwinstall.d/swim/lib/xwinstall.tcl --
No protocol specified
No protocol specified
application-specific initialization failed: couldn't connect to display ":0.0"
NOTE: initial log file: /tmp/install.log
  ***  Fatal error  ***  

No display
Current display is set to :0.0
Change the environment variable DISPLAY or restart this program as
/tmp/selfgz27981/install --display HOSTNAME:0
(with the appropriate hostname)

Exiting ...

Details:
Current display is set to :0.0
Change the environment variable DISPLAY or restart this program as
/tmp/selfgz27981/install --display HOSTNAME:0
(with the appropriate hostname)

Exiting ...
    while executing
"::rootwin::checkTkPresent"
    (procedure "::rootwin::init" line 2)
    invoked from within
"::rootwin::init"
    (procedure "MainProgram" line 13)
    invoked from within
"MainProgram"

auto_path = /tmp/selfgz27981/linux/tcl-8.6.9/lib/tcl8.6 | /tmp/selfgz27981/linux/tcl-8.6.9/lib | /tmp/selfgz27981/linux/tk-8.6.9/lib | /usr/local64/tcl-8.6.9/lib
The previous message has also been saved to /tmp/install.log

Answer 1

I happen to have a blog that is quite focussed on getting Bruker Topspin to work on Ubuntu and I have just made a blog post that should solve your problem. See: https://selkieupsilon.blogspot.com/2020/06/installing-bruker-topspin-4-on-ubuntu.html (I came across your question while looking at the top search results on "Ubuntu + Topspin")

Advice: If you are intending to use your computer for lots of NMR processing and analysis/research/scientific work, I strongly suggest you to upgrade to the 20.04 long term support LTS version as N0bert has suggested in the comments. The support cycle of the LTS is much more compatible with the stability you would need for a production machine compared to the in-between releases. Using a LTS means that you can continue to work, without needing to upgrade to the next release, in a stable environment, for at least 5 years; the in-between releases would require you to upgrade in ~9 months from the date of release, with part of your workflow potentially breaking every update. If you are new to Ubuntu, be aware that not every release is an LTS. I only use LTS releases for my work computers and that is the main reason why I only cover LTS releases in my blog posts.

I cannot guarantee that the rest of the commands below would work in 19.10, as I did not test 19.10. So I strongly recommend you to first upgrade to 20.04 before trying the installation again.

To answer your specific question, the command you ran (I'm assuming as root) would not work because root cannot be used to run graphical applications in the same way as in 18.04. I did not do a full troubleshoot on the reason, but I suspected it may be related to how $HOME is differently handled from 19.10 onwards.

Unfortunately, the (proprietary) Topspin installer is graphical. So you need to use the PolicyKit approach to run the graphical installer with elevated permissions/as root (PolicyKit approach taken from this blog post).

# pkexec env DISPLAY=$DISPLAY XAUTHORITY=$XAUTHORITY topspin-4-0-8-linux.sh

Just a warning that even after doing that and running the installation, it will not work immediately because Topspin requires another (proprietary) license manager called Codemeter Runtime and the DEB version is not bundled with the Topspin installer.

The installation of the Codemeter Runtime package is also unfortunately not straightforward under 20.04 (and I suspect also 19.10). I have covered how to install it on my blog. But briefly, you would need to install the equivs package to generate a dummy multiarch-support package, and I modified the instructions from this blogpost.

I'm happy to help troubleshoot if you run into further problems while retrying the installation under 20.04.

Answer 2

I ran into the same issue trying to install TopSpin 4.1.1 on a Fedora machine. Since running pkexec as non-root doesn't do the trick for me, I decided to just run it as root in a spawned shell:

# extract to get access to the installation script
bash topspin-4.1.1.2-linux.sh --keep --noexec
    
# actual installation
local flags="--nmradminpw topspin --setup-type po --gcc-off --auto"
sudo -- su -l -c "cd $PWD; topspin/install --nmrsu $(whoami) $flags"
    
# cleanup
rm -r ./topspin

# put a topspin command into our path (linking doesn't work!)
cat <<-EOF | sudo tee /usr/local/bin/topspin > /dev/null
    #!/usr/bin/env bash
    gnome-terminal -- /opt/topspin4.1.1/prog/bin/topspin
EOF
sudo chmod 755 /usr/local/bin/topspin

Running the install command without the leading sudo -- will fail. However this automatically extracts TS, installs it, and generates a wrapper script so it can be started with by typing topspin. No need to pollute my PATH.

Answer 3

Without pkexec, it worked for me if I did the install under root, that is, start by opening a terminal and type:

sudo su -

and then:

sh topspin-4.0.9-linux.sh

Answer 4

Just in case someone also has the issue that they have requested their (academic) license but don't know what to do with that generated key (and the Install license ticket button only gives an error):

You have to go to http://licensecentral-bbio.bruker.de/, enter your token there and then install the TopSpin license onto your local CodeMeter installation via that web page. After that restart TopSpin and everything should be working.

Answer 5

I encounter the same problem! The reason on this problem is user "root" can't connect GUI in this mode. Enable the user "root" and login in the ubuntu GUI using the user "root". Then you can install topspin normally(sh topspin-4.0.9-linux.sh).