HI Tim,
On Mon, 7 Oct 2019, Tim Gruene wrote:
Date: Mon, 07 Oct 2019 23:04:28 +0200
From: Tim Gruene <[email protected]>
To: Peter Keller <[email protected]>
Cc: [email protected]
Subject: Re: [ccp4bb] Shelx and debian 10
@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.
You're right, I wrote my reply to Bernhard too rapidly, and conflated
two separate issues. Debian 10 still supports static binaries of course,
but in its default configuration (without vsyscall=emulate), those
static binaries must be linked with a version of glibc that doesn't
require vsyscalls. OTOH, dynamic binaries don't suffer from this
problem, because they can use vDSO provided by the running (rather than
the build) system.
I think that part of the problem is that traditionally when we want to
build portable linux binaries, we tend to build on the oldest
distribution that we want to support, relying on backwards compatibility
to provide the portability that we are after. We often build statically,
because it is a robust way of including all the required libraries and
is less fiddly and error-prone than providing them as dynamic libraries.
There is also no danger of breakage caused by rogue values of
LD_LIBRARY_PATH (which users shouldn't be setting of course, but we have
no way of stopping them). The drawback of this approach is that when
backwards compatibility is broken, there is no application-level fix.
These kinds of problems are rare, but when they do happen the onus is on
those of us who distribute binary applications to find solutions. Some
sysadmins may have good reasons for being reluctant to change kernel
parameters to get third-party applications to work.
Regards,
Peter.
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/
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