Dear Bernhard,
We had this issue drawn to our attention last year by an early adopter
of Debian 10 while it was still in testing. I thought that it was a bug,
and submitted a report accordingly here:
<https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=889965>. I was told
that it is not a bug, but a feature ;-)
If you are able, you could try setting the kernel parameter
vsyscall=emulate. In the longer term, SHELXC/D/E will have to be rebuilt
to support systems where the vsyscall has been disabled. This means they
have to be dynamic executables that include the following in the output
of 'ldd':
% ldd /bin/bash
linux-vdso.so.1 (0x00007fff50952000)
....
All current distros use vDSO, so this shouldn't cause portability
problems by itself, but handling dynamic executables can be trickier
than static ones.
For a little more background, see <https://lwn.net/Articles/446528/>
Finally, you have my commiserations: although this change has been a
long time coming, it hasn't attracted a lot of attention. It was bound
to catch users of static executables by surprise.
Regards,
Peter.
On 07/10/2019 16:05, Bernhard Rupp wrote:
Hi Fellows,
we updated to Debian 10 on the local workshop computers, and reinstalled
Coot and ccp4. All fine.
Problem: Shelxc/d/e/ does not run, and
the call exits immediately sans any message.
This holds for the binaries included in ccp4 as well as for those from
the SHELX site.
The executables from CCP4 and SHELX site – same file size, probably
same - run fine under Debian 9.
I suspect a library problem.
Does some kind soul have CDE binaries for Debian 10 to share?
Many thx in advance, BR
----------------------------------------------------------------------------------------
Bernhard Rupp
Department of Genetics and Pharmacology
Institute of Genetic Epidemiology
Medical University Innsbruck
Schöpfstrasse 41
A 6020 Innsbruck – Austria
+43 (676) 571-0536
[email protected]
----------------------------------------------------------------------------------------
k.k. Hofkristallamt
San Diego, CA 92084
001 (925) 209-7429
[email protected]
[email protected]
http://www.ruppweb.org/
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