Dear Tim, Victor and Peter, Thank you for your quick reply! I found some of the posts you mentioned, but wasn't sure if it was related and how to change the parameters.
For those googling after me: close your wsl distro in windows: make a file with a texteditor that is able to do a utf8 encoding (e.g. notepad++) %userprofile%/.wslconfig (e.g. C:\Users\yourname\.wslconfig) and add the following lines: [wsl2] kernelCommandLine = vsyscall=emulate in powershell execute wsl --shutdown then restart your wsl-distro and it should state something like this when typing cat /proc/cmdline initrd=\initrd.img panic=-1 pty.legacy_count=0 nr_cpus=16 vsyscall=emulate If your distro does not start it is probably due to wrong formatting of the .wslconfig file. This solved both my arp warp and my shelx problem. Cheers, Johannes Am Mo., 7. Dez. 2020 um 15:02 Uhr schrieb Peter Keller < pkel...@globalphasing.com>: > 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 > >> > >> ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >> > >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > >> available at https://www.jiscmail.ac.uk/policyandsecurity/ > > > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
