Dear Bernhard and Peter, as Tim describes, changing the grub loader fixes the problem. I have looked into the changes to eliminate system calls and provide a version that would work without changes to the system, they are relatively minor. SHELXE just needs to eliminate calls to system time, pity for the convenient profiling but it can still be an option to be activated with the appropriate kernel. I just checked that the static version compiled with this change works perfectly on Debian 10. SHELXD in addition would need to get the number of threads as an input parameter rather than use what it detects in the system. We could shift to the interfaces the tasks of finding out the number of cores (and passing some time information to record in the output). The parameter already exists (-t) and users still fond of a terminal and command line usually know how many cores their machines have.
Up to George of course, whether he wants us to provide these versions and by when. Maybe he favours other alternatives. Best wishes, Isabel > ------------------------------ > > Date: Mon, 7 Oct 2019 17:05:44 +0200 > From: Bernhard Rupp <hofkristall...@gmail.com> > Subject: Shelx and debian 10 > > 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 > > bernhard.r...@i-med.ac.at > > > ---------------------------------------------------------------------------- > ------------ > > k.k. Hofkristallamt > > San Diego, CA 92084 > > 001 (925) 209-7429 > > b...@ruppweb.org > > b...@hofkristallamt.org > > 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 > > ------------------------------ > > Date: Mon, 7 Oct 2019 16:53:44 +0100 > From: Peter Keller <pkel...@globalphasing.com> > Subject: Re: Shelx and debian 10 > > 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 > > > > bernhard.r...@i-med.ac.at > > > > > ---------------------------------------------------------------------------------------- > > > > k.k. Hofkristallamt > > > > San Diego, CA 92084 > > > > 001 (925) 209-7429 > > > > b...@ruppweb.org > > > > b...@hofkristallamt.org > > > > 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 > > > -- > Peter Keller Tel.: +44 (0)1223 353033 > Global Phasing Ltd., Fax.: +44 (0)1223 366889 > Sheraton House, > Castle Park, > Cambridge CB3 0AX > United Kingdom > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ------------------------------ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ------------------------------ > > Date: Mon, 7 Oct 2019 23:04:28 +0200 > From: Tim Gruene <tim.gru...@univie.ac.at> > Subject: Re: Shelx and debian 10 > > 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 > -- > ICREA Res. Prof. Isabel Usón Crystallographic Methods Department of Structural Biology (“Maria de Maeztu” Unit of Excellence), Molecular Biology Institute of Barcelona, Spanish Research Council; Barcelona Science Park, Helix Building, 08028 Barcelona (Spain) http://chango.ibmb.csic.es/ARCIMBOLDO ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
