Singularity on Octopus

Arun added singularity to /usr/local/bin

octopus01:~$ /usr/local/bin/singularity shell shub://vsoch/hello-world
Progress ||----------------------------------|   0.0%
Progress |===================================| 100.0%
Singularity: Invoking an interactive shell within container...

Singularity vsoch-hello-world-master-latest.simg:~>
Singularity vsoch-hello-world-master-latest.simg:~> hello
bash: hello: command not found
Singularity vsoch-hello-world-master-latest.simg:~>
Display all 727 possibilities? (y or n)
Singularity vsoch-hello-world-master-latest.simg:~> less -V
less 458 (GNU regular expressions)
Copyright (C) 1984-2012 Mark Nudelman
Singularity vsoch-hello-world-master-latest.simg:~> cat /etc/issue
Ubuntu 14.04.6 LTS \n \l

Note that the `less -V` is likely older than on your system! Check the versions.

/usr/local/bin/singularity pull shub://vsoch/hello-world
Progress |===================================| 100.0%
/usr/local/bin/singularity exec vsoch-hello-world-master-latest.simg less -V
less 458 (GNU regular expressions)
Copyright (C) 1984-2012 Mark Nudelman

will run the singularity version. Now to see if slurm works:

/usr/local/bin/srun -N 1 --mem=32G --pty /bin/bash
/usr/local/bin/singularity exec --no-home vsoch-hello-world-master-latest.simg less -V
less 458 (GNU regular expressions)
Copyright (C) 1984-2012 Mark Nudelman

And it should work. If you get an error like 'ERROR: Home directory is not owned by calling user: /' it means we need to add a user account on octopus (uid in /etc/passwd on each node)

Create singularity image from guix package

guix pack -f squashfs -S /bin=bin pangenomes bash-minimal --tune=native

To cross-compile you could use, for example, --tune=skylake-avx512. Note this will only build on a machine that has the full skylake (or newer) instructions. E.g. tux05 EPYC 9274F is Zen 4 (Genoa), which supports AVX-512. The skylake-avx512 tuning level maps to x86-64-v4 (AVX-512F, AVX-512BW, AVX-512CD, AVX-512DQ, AVX-512VL), all of which Zen 4 supports. You could also use -march=znver4 for GCC to get Zen 4-specific optimizations, but skylake-avx512 / x86-64-v4 is the safe portable choice that works on both Intel and AMD with AVX-512.

/usr/local/bin/singularity shell bwxxlq1a7y02rcz1323xh1368l0w8h9s-pangenomes-bash-minimal-squashfs-pack.gz.squashfs