Dear Bernhard, as Peter mentioned, you need to reboot the system with the kernel parameter vsyscall=emulate. On Debian, you edit the file
/etc/default/grub and modify the value of GRUB_CMDLINE_LINUX_DEFAULT="quiet vsyscall=emulate" (default here is GRUB_CMDLINE_LINUX_DEFAULT="quiet") Once saved,you run the command 'update-grub' and reboot the system. @Peter: are you sure that without 'vsyscall=emulate' linux binaries need to be dynamically linked? I would be very surprised if the linux kernel would disable statically linked binaries. I rather think that the vanilla versions of shelx c/d/e (from shelx.uni-goettingen.de) are compiled with an obsolete compiler / obsolete compiler options. Best regards, Tim On Monday, October 7, 2019 5:53:44 PM CEST Peter Keller wrote: > 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/ > > > > ----------------------------------------------------------------------- > > > > > > ------------------------------------------------------------------------ > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
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