At ENC, I heard from a usually highly reliable source that Bruker will likely
be supporting Alma Linux going forward, with the demise of CentOS. For some
years, I have been running both Bruker Topspin and Varian OpenVnmrJ systems
on CentOS 7, and using one OS can have benefits. After I heard that, I
installed Alma Linux 8 on an old workstation, compiled OpenVnmrJ on it and
installed it, and connected it to a spectrometer to see what would happen.
It all worked fine.
With this recent AMMRL thread, I was curious to see what would happen with
the older Topspin versions and the new Alma Linux—I don't have any
consoles that old right in my own lab, but I have been planning to help someone
at a nearby institution update their Linux on an AV II system. So I tried
installing Topspin 3.2pl7 and Mestrenova on Alma 8. Without an immediately
available AV II console to experiment on, I just did a data processing
installation. But with the OpenVnmrJ already installed (which runs a script
to install all its dependencies automatically), I found I only needed one
more package for Topspin, and one more for Mestrenova's RHEL 8 version.
Mestrenova needed unixODBC-2.3.7-1.el8 (64 bit version) and Topspin needed
libXft-2.3.3-1.el8.i686 (32 bit version) which included a few dependencies
with that single install.
The old Topspin does want old network interface names (like eth0, eth1) and
as I recall those disappeared from CentOS between versions 5 and 7. I know
there's some workaround for that which I had to use several years ago updating
an AV III HD from CentOS 5 to 7, in order to use network interface names like
enp9s0, and I hope/expect it would still work.
I'm not sure how many unsatisfied package dependencies there would have been
without having OpenVnmrJ already installed, but I think that part of the OVJ
installation could be run without doing the complete install (it brings
in hundreds of packages on top of a vanilla Alma installation, I wouldn't
really care to attack those one at a time).
As for the larger question of whether I want a wall to wall Alma Linux lab
... I'm still undecided. I have one Varian system running OVJ under Ubuntu
22, and I think that's a fabulous combination. It's still one year and 21 days
until CentOS 7 reaches end of life ...
________________________________
> From: main_at_ammrl.groups.io <main_at_ammrl.groups.io> on behalf of Todd Rappe v=
> ia groups.io <rapp0006=umn.edu_at_groups.io>
> Sent: Friday, June 9, 2023 10:19 AM
> To: main_at_ammrl.groups.io <main_at_ammrl.groups.io>
> Subject: Re: [AMMRL] Software /Operating system Upgrade on 400MHz DRX System
Info on the 32-bit libraries can be found at
https://repo-bbio.bruker.com/CentOS/7/TopSpinInstallationRequirements.html
Also, the following info was on the Bruker Knowledge base for TS 2.1. Not sure
if it applies to 1.3. Unfortunately, this useful resource is no longer available
for customers to search.
Item #13458 -- Required Modifications for TopSpin 2.1pl8 on CentOS 7.1
Item#: 13458 Opened: October 1, 2015 Status: FAQ Severity: non-critical
OS/Version: LINUX Program: TOPSPIN Component: configuration Version: 2.1.8
Solved in: not solved
Instrument: any Hardware Unit: any Hardware Group: any Summary: Required
Modifications for TopSpin 2.1pl8 on CentOS 7.1
Description:
Workflow to install TopSpin 2.1pl8 on CentOS 7 64 bit
1. CentOS should be installed according to
ftp://ftp.bruker.de/pub/nmr/CentOS/7/TopSpinInstallationRequirements.html
In addition to the packages mentioned there, the package
bruker-compatlibs must be installed.
2. TopSpin 2.1pl8 is not compatible with the Network Manager and the Firewall
setup used on CentOS 7. Therefore it is strongly advised to use the flexlm and
diskless package of TopSpin 3.2pl7 or newer and not the packages coming with
2.1pl8! Install TopSpin 3.2pl7 with diskless and flexlm, then install TopSpin
2.1pl8 with the desired packages but do NOT install diskless and flexlm again!
3. After the successful installation of TopSpin 2.1, some modifications must
be applied: a) remove ld version 2.16.1
cd /opt/topspin/gnu
find . -name ld -exec mv {} {}.org \;
(OS-provided ld version 2.23.52 is used now to link the object files)
b) replace the makeau script with the attached version according to the also
attached installation instruction
4. To allow cf to create hardlinks, the kernel hardlink protection must deactivated
(otherwise only links to files with same owner are allowed):
Switch off the link protection in
/usr/lib/sysctl.d/50-default.conf
change
fs.protected_hardlinks = 1
fs.protected_symlinks = 1
to
fs.protected_hardlinks = 0
fs.protected_symlinks = 0
(See Item 13814)
In some cases TopSpin 2.1 hangs during startup after showing the splash screen.
This can be caused by some configuration in the /home/<user name>.topspin* folder
if a newer TopSpin version was started before. After removing this folder,
TopSpin 2.1 should start.
Update:
The Topspin installation information for CentOS 7 is no longer available at
ftp.bruker.de (See Item 14537)
The relevant info can now be found at
http://bruker.telemaxx.net/student/CentOS/7/TopSpinInstallationRequirements.html
___________________________________
Todd Rappe
Minnesota NMR Center <nmr.umn.edu<
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612-625-9147 (office)
651-321-TODD (rings office and mobile)
612-624-8892 (magnet lab)
On Fri, Jun 9, 2023 at 12:03 PM DrSpin <rajanp_at_uw.edu<mailto:rajanp_at_uw.edu>> wrote:
Hello Nadia
We are running TS1.3PL10 successfully on a CentOS 7 system. You may have
to put some effort in gathering the 32 bit libraries to make it work, though.
Best of Luck.
Regards
Rajan
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Received on Fri Jun 09 2023 - 11:14:54 MST