CNS in arm bartender docker image un-runnable

[sverhoeven]

Image from https://github.com/i-VRESSE/haddock3-webapp/pkgs/container/bartender

docker run --platform linux/arm64 --entrypoint bash --rm -ti  ghcr.io/i-vresse/bartender:latest
name -a
Linux 2c6d524f6d00 6.8.0-48-generic #48-Ubuntu SMP PREEMPT_DYNAMIC Fri Sep 27 14:04:52 UTC 2024 aarch64 GNU/Linux
find /venv/ -name cns
/venv/lib/python3.9/site-packages/haddock/bin/cns
ldd /venv/lib/python3.9/site-packages/haddock/bin/cns
/venv/lib/python3.9/site-packages/haddock/bin/cns: /lib/aarch64-linux-gnu/libm.so.6: version `GLIBC_2.38' not found (required by /venv/lib/python3.9/site-packages/haddock/bin/cns)
/venv/lib/python3.9/site-packages/haddock/bin/cns: /lib/aarch64-linux-gnu/libc.so.6: version `GLIBC_2.38' not found (required by /venv/lib/python3.9/site-packages/haddock/bin/cns)
        linux-vdso.so.1 (0x0000400000801000)
        libm.so.6 => /lib/aarch64-linux-gnu/libm.so.6 (0x0000400036010000)
        libmvec.so.1 => not found
        libc.so.6 => /lib/aarch64-linux-gnu/libc.so.6 (0x00004000360b0000)
        /lib/ld-linux-aarch64.so.1 (0x000071608702c000)

dpkg -s libc6
...
Architecture: arm64
Multi-Arch: same
Source: glibc
Version: 2.36-9+deb12u8
...
cat /etc/os-release
PRETTY_NAME="Debian GNU/Linux 12 (bookworm)"
...

In libc-2.38 libmvec was added. Also see file listing at https://debian.pkgs.org/12/debian-main-arm64/libc6_2.36-9+deb12u9_arm64.deb.html and https://ubuntu.pkgs.org/24.04/ubuntu-main-arm64/libc6_2.39-0ubuntu8_arm64.deb.html

Solutions:

1. the cns executable should be compiled with libc 2.36 . After recompile and upload to SURFDrive, the cachebust line at

   haddock3-webapp/deploy/Dockerfile.bartenderhaddock3

   Line 69 in a56f87d

   RUN echo cachebust=14 && git clone --depth 1 -b ${HADDOCK3_VERSION} https://github.com/${HADDOCK3_GHORG}/haddock3.git .

   must be bumped and a new haddock3-webapp release must be made.
2. the docker image should have libc >=2.38 like Ubuntu 24.04. The Docker image of https://github.com/haddocking/haddock3/blob/main/Dockerfile will also need an OS upgrade.

[amjjbonvin]

Thanks Stephan I recompiled CNS in a Debian system and now it works fine as is.