SAM - Software and Modules

This repo contains some programs used to generate the containerized build environments used by the software and modules working group at the ASC Research Center. The sam working group uses EESSI¹ as a base for the software stack that is provided on the MUSICA cluster.

crtar

This is a simple program that can be used to create tarballs, it is based on a bash function defined in the build_container.sh script used on the harbok cluster at University of Groeningen².

samctr

A simple wrapper around some apptainer commands. Why the wrapper? The use case that is being targeted by samctr is to create a portable build environment for cvmfs³ repositories, ahead of publishing newly built software to a stratum0.

Part of the motivation for creating this program was to make it easier to submit software build + publish jobs as sbatch scripts.

Most of the login implemented in samctr is derived from the eessi_container.sh script authored by Thomas Roeblitz⁴.

Installation

samctr

go install github.com/asc-ac-at/sam/cmd/samctr@latest

crtar

go install github.com/asc-ac-at/sam/cmd/crtar@latest

Examples

config.yaml

samctr will look for a config file (in order of precedence) at:

• the path specified after the --config or -f flags
• $XDG_CONFIG_HOME/samctr/config.yaml
• $HOME/.config/samctr/config.yaml

A config file can be used to configure various options that will be passed through to the apptainer commands later run by the program. For example, the following will pull a specific image create a sif file therof, set up a bind mount for host_injections and (read only) fusemounts for a number of cvmfs. Additionally, a writeable overlay for one of these repositories is set up. Also any nvidia gpu found on the host will be passed through to the container.

image: "docker://registry.somewhere/builder-rocky96:24601"
host_injections: /opt/alt/eessi
fusemounts:
  - type: "container"
    fuse_cmd: "cvmfs2"
    fuse_arg: "cvmfs-config.cern.ch"
    ctr_mountpoint: "/cvmfs/cvmfs-config.cern.ch"
  - type: "container"
    fuse_cmd: "cvmfs2"
    fuse_arg: "software.eessi.io"
    ctr_mountpoint: "/cvmfs/software.eessi.io"
  - type: "container"
    fuse_cmd: "cvmfs2"
    fuse_arg: "speedy.repo"
    ctr_mountpoint: "/cvmfs_ro/speedy.repo"
nvidia: all
writeable_repos: ["speedy.repo"]
fuse_cmd_rw: fuse-overlayfs

shell

This can be used to launch an interactive shell with a specific config.

$ samctr shell --config=/tmp/min-conf.yaml

exec

This wraps the "apptainer exec" command, the -- seperator is used to signify what should be passed on to apptainer exec as program arguments.

simple command

$ samctr exec -- ls /cvmfs

interpret an arbitrary script

$ cat hello_world.py | samctr exec -- python3

Build piece of software

$ cat >build_go_1250.sh <<EOF
#!/bin/sh

export EESSI_PROJECT_INSTALL=/cvmfs/software.asc.ac.at
source /cvmfs/software.eessi.io/versions/2023.06/init/lmod/bash
source /cvmfs/software.eessi.io/versions/2023.06/init/bash
module load EESSI-extend
eb -r Go-1.25.0.eb
EOF
$ samctr exec -- /bin/sh <build_go_1250.sh

Submit a build as a slurm job

Define a build script something along the following lines

> cat build_go1250_jobscript.sh
#!/bin/sh
#SBATCH -p zen4_0768
#SBATCH --mem=64G
#SBATCH --ntasks=1

# Define a build command to pass into the container
cat >tmp_build_cmd.sh << EOBC
#!/bin/sh
export EESSI_PROJECT_INSTALL=/cvmfs/software.asc.ac.at
source /cvmfs/software.eessi.io/versions/2023.06/init/lmod/bash
source /cvmfs/software.eessi.io/versions/2023.06/init/bash

module load EESSI-extend
eb -r Go-1.25.0.eb

# Create tarabll shared directory to access after job completion
crtar -name Go-1.25.0 -outputDir /opt/adm/sw-archives
EOBC
chmod +x tmp_build_cmd.sh

# run the "build_cmd" in apptainer with default config
samctr exec -- /bin/sh <tmp_build_cmd.sh

# cleanup
rm -f tmp_build_cmd.sh

submit the job with sbatch:

sbatch build_go1250_jobscript.sh

Footnotes

Footnotes

1. European Environment For Scientific Software Installations https://eessi.io ↩

2. https://gitrepo.service.rug.nl/cit-hpc/habrok/cit-hpc-easybuild/-/blob/main/jobscripts/habrok/build_container.sh?ref_type=heads ↩

3. Cern VM-FS https://cernvm.cern.ch/fs/ ↩

4. https://github.com/EESSI/software-layer-scripts/blob/main/eessi_container.sh ↩