Dear Johannes,
On 07/12/2020 13:21, Tim Gruene wrote:
Dear Johannes,
w.r.t. shelx-binaries:
you can check with
#> cat /proc/cmdline
whether the linux-kernel option include 'vsyscall=emulate'.
Quite some time ago, the linux kernel made vsyscall obsolete. The
SHELX-binaries are probably compiled with an old compiler on an
old linux system, and require this kernel option to run.
There has been some correspondence about this on the CCP4 list in
October last year, in the context of static executables not working on
Debian 10. The thread starts here:
<https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;e91ed61d.1910>,
and my own substantive reply is here:
<https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1910&L=CCP4BB&D=0&P=44830>.
Tim is right. Traditionally, compiling static executables on an old
system is a technique used to try to ensure compatibility with newer
distributions, on the basis that building on a new system is more likely
to break with older systems than the other way around.
However, when kernel options like this are changed so as to break
backwards compatibility, then building static executables on an old
system ensures INcompatibility with newer systems.
Otherwise they trigger a segmentation fault.
vsyscall's are considered a small security hole, but unless you run a
safety-critical machine, you can probably risk to open this hole in
your kernel at the benefit of running the SHELX programs.
That is a decision for you of course. This may not be an option for
everyone though. The universal solution is for SHELX executables that
don't require vsyscall to be made available, but we rely on the SHELX
maintainers for that.
Regards,
Peter.
This link might be related:
https://github.com/microsoft/WSL/issues/4694
Cheers,
Tim
On Mon, 7 Dec 2020 13:50:23 +0100
Johannes Cramer <johannes.cra...@gmail.com> wrote:
Dear board,
has anyone gotten ccp4 (specifically shelx and arpwarp) installed and
working under wsl2 (windows subsystem for linux)?
arp warp refuses to install with the following error:
Segmentation fault
*** ERROR ***
This machine cannot run ARP/wARP executables that
are statically linked to glibc.
shelx does not complain during installation, but when I type shelxc
(or shelxd, shelxe, shelxl, shelxt) I get immediately to the promt.
No error message or anything.
I am using Ubuntu 20.04 LTS.
Any help would be appreciated.
Cheers,
Johannes
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